Thank you, Mike.
As this is a project for work, I can't send the animations to you. But yes, the assets are used in animations and one workaround that I found was to add an animation and drag every asset into it. This does put them into the new scaled project. I need to test this more to find out if it actually works in all scenarios. Right now it's a pain to add multiple assets to the animation, since you can only drag them one at a time and our project is quite large.
EDIT: It didn't work for everything. Some of the assets were still left out from the new project. I've checked the file names and such, but there isn't any consistency in the files that would suggest naming problems.
EDIT2: I found out that there were some file extensions missing. That combined with the solution above did the trick.
/Idiot