Done that. I understand the file limit is 1000MB, but it stipulates a limit to the NUMBER of files. My game is 300MB but almost 2000 files.
Ah ok I understand you now. Make sure if you upload the game manually to create a single zip file or you can use alternative the buttler command line tool. Generally you should be uploading one file, a zip file, that compresses all other files. Other than that I cant see why Itch.io would have a problem with the number of files your game uses. Is it a browser game ?