Maschine saves the favourites to the following location:
C:\Users\YOUR USER NAME\AppData\Local\Native Instruments\Shared
If you had deleted this when you reinstall everything as you mentioned, then it will not be possible to reinstate those favourites. You could try restoring a Windows backup to just before you made those changes, and then save that favourites file from the above location. On a reinstall, you then simply place your favourites file in the above location.