With Version 3.07 onwards, I have decided to instead upload the game uncompressed. For minor bug fixes, you will only need to download the "Data" folder instead of the whole thing, and replace the one you have. You can check if it is up to date by the name of the uploaded folder. For example if you have reported a bug in version 3.07 and the uploaded folder is now named "Version 3.08", that means the Data folder probably has the solution you need.

Do tell me how this works out for you. It's way faster on my end than compressing the entire thing every time and then uploading everything.