Okay, so if we back up a bit ...
- you upgraded to 1.3.9c
- after that you were somehow hacked, presumably by something that was left on the server from the old vulnerable version, or maybe from something completely outside of your Zen Cart site.
- then you restored files from an old 1.3.8 backup
- then it told you it's out of date
- now you're trying to simply get the 1.3.9c files back onto the server
So, where is the copy of the 1.3.9c files you prepared for uploading to the server (with customizations and merging etc) on the day that you upgraded the server to 1.3.9c? I would expect that you have a copy of all those files at least on your PC someplace (assuming you actually did the file merging, comparisons, customizations, etc on your PC before uploading to the live site), or even better yet, you'd have a full copy of those files and a duplicated testing database, all in another spot on that or another server, for testing the upgrade to be sure it's all working right before taking all the updated files to the live server and upgrading the database. That's how the published upgrade instructions advise upgrades to be done.
Now, if the hack happened as a result of some old vulnerable files being left on your server which didn't belong, then those definitely need to be cleaned out and removed from the server. That's all part of the Recovering From Hack Attempts instructions which are posted in the wiki and in the Hack Attempts discussion area of the forum.
If for some reason you don't have a good set of merged 1.3.9c files on your PC from what went onto the server, then I recommend simply doing the upgrade process over again, to prepare a good set of clean customized files. Then, after making a backup of the server contents, wipe out the Zen Cart files/folders from your server, and upload the new set of files to the server. You'll want to be sure that you don't delete your images, etc, but you do need to make sure that all the files in all your images folders are actually images, and not PHP files or contain something other than pictures even if they have a ".jpg" or whatever extension on them. Make no assumptions. It's all part of cleaning up from hacks.
As you were told in the other thread you mentioned, there's no database changes from v1.3.9a to b to c to d, so you shouldn't need to rerun the database-upgrade component at this time.
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