I've run into a big issue in my code.
TL;DR: After a few comments, I decided to post the entire code here:
https://repl.it/repls/AustereShinyBetatest
Here's my code:
def highlight_nonmodified(content: str) -> str:
    regex = re.compile(r'(?s)(\{.*?[^\}]+\})', re.I | re.S)
    replace = r'#\1'
    content = regex.sub(replace, content)
    return content
def get_line(string_t: str, original: str) -> int:
    original = original.splitlines(True)
    for (i, line) in enumerate(original, 1):
        if string_t[1:] in line:
            return i
    return -1
def highligh_merge(original: str, modified: str) -> str:
    for line in modified.splitlines(True):
        if line.startswith('#'):
            numer = get_line(line, original)
            error = r"#Tag not supported at line{0}\n".format(numer)
            error = error + line
            modified = modified.replace(line, error)
My issue is that here's what happens:
Textfile.txt (original):
1. Here goes some text. {tag} A wonderful day. It's soon cristmas. 
2. Happy 2019, soon. {Some useful tag!} Something else goes here. 
3. Happy ending. Yeppe! See you. 
4. 
5  Happy KKK! 
6. Happy B-Day!
7 
8. Universe is cool!
9.
10. {Tagish}. 
11.
12. {Slugish}. Here goes another line. {Slugish} since this is a new sentence. 
13.
14. endline.
Modified.txt:
Here goes some text.  A wonderful day. It's soon cristmas. 
Happy 2019, soon. #{Some useful tag!} Something else goes here. 
Happy ending. Yeppe! See you. 
Happy KKK! 
Happy B-Day!
Universe is cool!
. 
#Error: Tag not supported at line-1\n#{Slugish}. Here goes another line. #{Slugish} since this is a new sentence. 
endline. 
I cannot seem to get precise line numbering and comparing of lines, what am I doing wrong here, I am obviously, storing two copies, original and modified and then I pick then I try to pick out the line number from the original text by looping over line by line. But still without any success, is this even possible. Thanks a lot in advance!
I don't think this can be done if multi-line chunks of text may have been removed. However if you control the tagging process, you could include the original line number in the tag:
{ foo:12 }
and then recovering it is trivial
original = int(re.search(r'\d+', tag).group(0))
This modified version of your code:
import re                                                                                                                        
def annotate_tags(content: str) -> str:                                                                                          
    """Annotate tags with line numbers."""                                                                                       
    tag_pattern = re.compile(r'(\{(?P<tag_value>[^}]+)\})')                                                                      
    lines = content.splitlines(True)                                                                                             
    annotated_lines = []                                                                                                         
    for idx, line in enumerate(lines, 1):                                                                                        
        annotated_lines.append(tag_pattern.sub(r'{\g<tag_value>:%s}' % idx, line))                                               
    annotated = ''.join(annotated_lines)                                                                                         
    return annotated                                                                                                             
def modify(content: str) -> str:                                                                                                 
    supported_tags = {                                                                                                           
            re.compile(r'(\{tag:\d+\})'): r'',                                                                                   
            re.compile(r'(\{Tagish:\d+\})'): r''                                                                                 
    }                                                                                                                            
    for pattern, replace in supported_tags.items():                                                                              
        matches = pattern.findall(content)                                                                                       
        if matches:                                                                                                              
            content = pattern.sub(replace, content)                                                                              
    return content                                                                                                               
def highlight_nonmodified(content: str) -> str:                                                                                  
    regex = re.compile(r'(?s)(\{.*?[^\}]+\})', re.I | re.S)                                                                      
    replace = r'#\1'                                                                                                             
    content = regex.sub(replace, content)                                                                                        
    return content                                                                                                               
def get_line(string_t: str, original: str) -> int:                                                                               
    tag_pattern = re.compile(r'(\{[^}]+:(?P<line_no>\d+)\})')                                                                    
    match = tag_pattern.search(string_t)                                                                                         
    if match:                                                                                                                    
        return match.group('line_no')                                                                                            
    return -1                                                                                                                    
def highlight_merge(original: str, modified: str) -> str:                                                                        
    tag_regex = re.compile(r'#(?s)(\{.*?[^\}]+\})', re.I | re.S)                                                                 
    for line in modified.splitlines(True):                                                                                       
        if tag_regex.search(line):                                                                                               
            numer = get_line(line, original)                                                                                     
            error = "#Tag not supported at line{0}\n".format(numer)                                                              
            error = error + line
            modified = modified.replace(line, error)
    return modified
if __name__ == '__main__':
    file = 'textfile.txt'
    raw = ""
    with open(file, 'rt', encoding='utf-8') as f:
        for i, s in enumerate(f, 1):
            raw += "{}. {}".format(i, s)
    original = modified = raw
    modified = annotate_tags(modified)
    modified = modify(modified)
    modified = highlight_nonmodified(modified)
    modified = highlight_merge(original, modified)
    with open("modified.txt", 'w', encoding='utf-8') as f:
        f.write(modified)
Generates this output:
1. Here goes some text.  A wonderful day. It's soon cristmas. 
#Tag not supported at line2
2. Happy 2019, soon. #{Some useful tag!:2} Something else goes here. 
3. Happy ending. Yeppe! See you. 
4. 
#Tag not supported at line5
5. #{begin:5}
6. Happy KKK! 
7. Happy B-Day!
#Tag not supported at line8
8. #{end:8}
9. 
10. Universe is cool!
11. 
12. . 
13. 
#Tag not supported at line14
14. #{Slugish:14}. Here goes another line. #{Slugish:14} since this is a new sentence. 
15. 
16. endline.
Below is a short script to import the files, clean the data, create enumerated dictionaries, and output results (optional based on print_results variable).
(If I'm not interpreting your question correctly, please let me know!)
import re
from os import path
"""
Create an error class for trying to close a file that isn't open.
"""
class FileException(Exception):
    pass
class FileNotOpenError(FileException):
    pass
"""
Input variables.  base_path is just the directory where your files are located.
If they are in different directories, then use a second variable.
"""
base_path = r'C:\..\[folder containing text files]'
original_filename = 'test_text.txt'
modified_filename = 'modified_text.txt'
def import_data(file_name, root=base_path):
    """
    Read each text file into a list of lines.
    """
    full_path = path.join(root, file_name)
    with open(full_path, 'r') as f:
        data = f.readlines()
    try:
        f.close()
    except FileNotOpenError:
        pass
    if len(data) > 0:
        return data
def remove_numbering(input):
    """
    RegEx to clean data; This will remove only the line numbers and not
    any subsequent number-period combinations in the line.
    """
    p = re.compile(r'^([0-9]+[.]?\s)')
    return p.sub('', input)
def text_dict(text_list):
    """
    Remove numbering from either file; Considers period punctuation following number.
    """
    new_text = [remove_numbering(i).lstrip() for i in text_list]
    return {idx+1:val for idx, val in enumerate(new_text)}
def compare_files(original, modified, missing_list=None):
    # Create a fresh list (probably not necessary)
    if missing_list is None:
        missing_list = list()
    # Ensure that data types are dictionaries.
    if isinstance(original, dict) and isinstance(_modified, dict):
        # Use list comprehension to compare lines in each file.
        # Modified line numbers will end up in a list, which we will return.
        modified_index_list = [idx for idx in original.keys() if original[idx] != modified[idx]]
    # Check to see if list exists; Return it if it does.
    # if len(modified_index_list) > 0:
    if not modified_index_list is None:
        return modified_index_list
def comparison_findings(missing_list, original_dict, modified_dict):
    print('Modifications found on lines:\n- ' + '\n- '.join([str(i) for i in missing_list]))
    print('\n\n\tOriginal:\n')
    max_len = max([len(original_dict[i].replace('\n','').rstrip()) for i in original_dict.keys() if i in missing_list])
    print('\t\t{0:^7}{1:^{x}}'.format('Line','Value',x=max_len))
    for i in missing_list:
        temp_val = original_dict[i].replace('\n','').rstrip()
        print('\t\t{0:>5}{1:2}{2:<{x}}'.format(str(i), '', temp_val, x=max_len))
    print('\n\n\tModified:\n')
    max_len = max([len(modified_dict[i].replace('\n','').rstrip()) for i in modified_dict.keys() if i in missing_list])
    print('\t\t{0:^7}{1:^{x}}'.format('Line','Value',x=max_len))
    for i in xyz:
        temp_val = modified_dict[i].replace('\n','').rstrip()
        print('\t\t{0:>5}{1:2}{2:<{x}}'.format(str(i), '', temp_val, x=max_len))
if __name__ == '__main__':
    print_results = True
    # Import text files.
    orig_data = import_data(original_filename)
    mod_data = import_data(modified_filename)
    # Create enumerated dictionaries from text files.
    _original = text_dict(orig_data)
    _modified = text_dict(mod_data)
    # Get a list of modified lines.
    mod_list = compare_files(_original, _modified)
    # Output results of file comparison.
    if print_results:
        comparison_findings(mod_list, _original, _modified)
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