Adding resources through the Resource Manager shouldn't corrupt the game. That's exactly how you're supposed to add them.
When you last Saved your project, did it complete the save successfully, or did the computer get shut down part-way through the save (power outage, or whatever)? Or did you have a network glitch during the Save?
When Saving a Steam-enabled project, I think it has to synchronize all of the resources to the Steam servers. I know when I had projects with that enabled, saves took a minute or so. I don't know what would happen if the save were interrupted.
If the other posters were right, your project should never have been visible as a ZIP file, even if under the covers, Steam does exactly that to synchronize the project.
I wonder if the synchronization got corrupted somehow. If it did, I think your game might have been lost.
What I would do is back up the local content for your game, then remove the local copy of the game and load it back from the Steam cloud. Does that do the same thing? Your projects live under your Documents\RPGVXAce folder. So:
1. Shut down RPG VX Ace
2. Move your project from that folder to a folder NOT under the RPGVXAce folder
3. Start RPG VX Ace
4. Use Manage Projects to load the Project from the Steam Cloud
I'm not 100% sure my directions are accurate, since I avoid using the Steam Cloud --- I don't like waiting a minute or more between saves and am worried the synchronization will have problems.