After running the tool and then loading my project, GameMaker said that all Texture Groups I had set up are missing and all sprites have been added back to the Default Texture Group.

I'm using IDE version 2023.2.1.75

Can confirm it also happens with the latest version. I also tried clearing the GM IDE Cache (both roaming and locallow) to check if it makes a difference. It only happens when AseSync is adding a completely new sprite. GameMaker wants to reload the project and when it is done, the Texture Groups are missing.

Please file a bug report here.