I purchased the Atari 50 collection and I would like to play it on Linux. I installed it with the Wine emulator seamlessly but it crashes on running. Then I browsed the install directory and found a gigantic 11GB "assets.pie" file, so I have no chance to extract the games and play them with an emulator. Is there a way to extract this "assets.pie"?

Found two ways that could work:
https://gist.github.com/WinterSnowfall/7d87ed156fb65896fdba6e925e54bb2a
https://github.com/farmerbb/RED-Project/issues/62#issuecomment-1326696288

Little update, doing everything through Linux:

Download https://github.com/Masquerade64/Cowabunga/releases/latest, extract the EXE, put it and assets.pie in the same and run: For the arcade games, extract the folder roms/Arcade from the output ZIP, download https://gist.github.com/WinterSnowfall/7d87ed156fb65896fdba6e925e54bb2a, place the downloaded JS file in the Arcade folder and run: For the other games, they're all in the roms folder.

And for the Atari Lynx BIOS file, open it on a hex editor, e.g. KDE's Okteta, and change the last F0 for 80.

So can I assume you got it working on linux?

By "it", you mean the tools for the extraction process, or the ROMs?

Both actually. Though I will assume there are always some "issues" somewhere

Been 8 months already, so I don't quite remember things clearly, but I don't remember having had issues.