Two relatively easy ways:
1) Go online, upload use file (as we have been discussing). This will get you online with the comments from the offline file, and the logic and data that is actually in the PLC. You won't lose anything. This copy can be saved with a new filename and it will be a good match and contain comments. If you save this file with the same name as an existing file, then of course you will lose what was in that file. Bottom line, you end up with the right logic, data and comments.
2) Open up your favorite version of the file with comments. Go to Tools, Database, ASCII Export. This brings up a dialog box that lets you pick what to export and how. The default is a native export with everything checked. Next, go online (Create New File). While online, go to Tools, Database ASCII Import. You will then have to chose the files you created earlier one at a time as RSLogix imports them. When finished it will report any conflicts. Don't forget to save the program after the import. Later, you can explore that Database export tool again and check out the csv tab. This lets you export address comments and symbols and file labels to a csv file which can be easily and powerfully edited in your favorite spreadsheet program, and then imported. It's a good way to mass edit, autofill, spell check, and more.