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Thanks for the fast reply! I already archived all my image, audio and rpy files, but the number of files barely changes.

Even my test project with no assets at all suddenly has more than 1.800 files... 

After extracting the .zip folder of my test project "Testing" (2 lines of dialogue, no images, no audio), I get these folders: game (93 files), lib (566 files), renpy (465 files) and (538 files). This project hits the file limit even though it has no content.

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You're definitely building your distribution incorrectly.

From the Ren'Py launcher (latest version), select your project but don't click Build Distributions.  Instead, click Web (Beta), then Build Web Application.  This creates a directory with a bunch of stuff including a file.  Ignore everything else and upload the file.  Correction: you need to upload the entire directory, packaged as a zip file.

The Build Distributions button is for building downloadable games, not web games.

Yes, that was the problem. This is my first time making a web game, so I didn’t know about the Web build. Thought it wouldn’t work since it‘s a beta version as well…

Anyway, problem solved! Thanks for the confirmation!