Definition of merge.
Definition of overwrite.
Basically the files in "affected_files_xxx" are core Zen Cart files (with path) already modified to work with their respective version of Zen Cart. If you have made any changes to these files (and uploaded the changes to your production server), you will need to "merge" your changes with the changes found in these files (best done on a local copy of the site). Once done with any needed file merging, you can simply upload the files (which overwrites the files on the server).
Note: Don't forget to BACKUP your production site before making any modifications. This includes both the database and files.
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