This issue can be solved by manually replacing the delimiter with a neutral string before formatting and then restoring the original delimiter.
The code shown below does the job. Any delimiter can be given as the argument of the IndentComments function so that it can be used with any type of code. The last line creates a map for calling the function set on latex by pressing '§'.
Just add it to your ~/.vimrc configuration file.
" Solve the issue of formatting comments " @param delimiter the comment delimiter for the chosen filetype" function! IndentComments(delimiter) range " set a temporary substitute for the delimiter let s:tmp_delimiter = 'delimiter>>>>' " replace the delimiter with the substitute exec a:firstline.','.a:lastline.' '.'s/'.a:delimiter.'/'.s:tmp_delimiter.'/' " reformat all lines in the range exec a:firstline.','.a:lastline.' '.'normal! ==' " put back the original delimiter exec a:firstline.','.a:lastline.' '.'s/'.s:tmp_delimiter.'/'.a:delimiter.'/' endfunction " mapping '§' to reformat selected code in latex :map <silent> § :call IndentComments("%") <CR>