Okay, what has probably happened is that when you went back online, RSLogix did not find the commented copy matched exactly with the files stored in the default path on your PC (which can happen for a variety of reasons).
So it prompted you to find the file or create a new one. You (or some other person using the PC) selected Create New File. This new file had no comments, but was later saved. It is now the best matching file that RSLogix can find when you go online, so RSLogix chooses it and does not even give you the chance to pick the correct one.
To fix this problem, figure out which file(s) on your PC have no comments and delete them (or move them out of the default directory).
Again, the PLC does not contain comments. They are ONLY stored on the programming PC, so find the file with RSLogix that still has the comments, and then go online. If RSLogix says "Matching file not found" don't create a new file, rather use the browse option to select the correct file you have identified and select "Upload Use File".
Paul