I had to move my initializing room back to the top of Room Order, and I worry some things might potentially have been lost when the GMS project tool converted the resource files back to their current version format (using IDE v2024.11.0.179 Runtime v2024.11.0.227) , but at surface level it looks to be working well so far outside changing the room order. I'll reply in this thread if any other bugs surface that seem to have resulted from using this tool on a more recent GMS project file.

Texture Group settings were reset. Had to uncheck "Automatically Crop" on the texture group I dedicated to sprites that shouldn't be auto cropped.

I had a quite similiar experience recently, I used it in a project that was corrupted and when opening it GameMaker showed the following message                                 

"This project is of an older format and will need to be converted. Proceed?"

Then I opened the project and one of main objects was gone just like that, it can be because when my computer shut down it was the object I was working on but it is what it is, I wish he updated the tool though..