Based on what you described, I assume you are using butler?
When uploading files with butler, the name of the zipped downloadable file doesn’t change, even if you change it locally when pushing the new version with butler. To change the zip’s name, you can go to “Edit Game” and when browsing your available files, select the name of the one you want to change, and rename that.
Deleting an older entry, and re-uploading one with a new name shouldn’t cause issues. The only issue I can think, is that the Itch app is trying to keep the game’s version updated based on the “Channel Name” that you’ve used. So if you deleted an older file, the app wouldn’t be able to update the game anymore. If the newly uploaded file has the exact same “Channel Name”, then I’m not sure if the Itch app can tell the difference.
Did you use the same “Channel Name” when you re-uploaded the game?
As a side note, make sure to use the “Reply” link below someone’s comment when replying to them, so they get a notification :)