Sorry to necro this post almost 4 years later, but I wanted to let anybody else who might be wondering about this know:
VaM stores favorites and hide files in the "AddonPackagesFilePrefs" folder in the equivalent path to where the file would be.
For example, if you have a "MyScene.json" scene file in a package called "NewCreator.DummyScene.1.var", a file will be created at AddonPackagesFilePrefs/NewCreator.DummyScene.1.var/Saves/scene/MyScene.json.fav when you favorite it. Similarly, a .hide (instead of .fav) will be created when you hide a file.
So, in essence the AddonPackagesFilePrefs folder _is_ the storage for your favorites and hidden files. I hope the OP discovered this before manually recreating it all... but mostly this is...