Thanks for the reply. I resolved most of the issues by deleting the collection, opening AssetForge to let it rebuild the thumbnail cache, closing it, then reimporting the collections. I think the "Do not put any other files in there" part was key to this problem. The ones that were broken had rogue .fbx files or folders that I copied over from the original pack (curiously they were empty folders named gITF, Materials, Textures). I just assumed AF would ignore anything that it couldn't read.
An interesting bug I noticed is if you create a collection folder with the same name as the default collection folders (e.g. Buildings), then your assets will show up in the default folder plus its own custom folder which is kind of nice. Would be great for AssetForge to just merge these and not have the duplicate Buildings folder in the custom collections section or bypass this altogether by allowing to add or remove assets from the default collections.