If you want to save all your other collections, you need to do this with collection.db file instead
Sup A Noob wrote:If you ever experience favourites deletion ingame, copy the osu! config file named after your computer into somewhere else while the game is still on. Then turn off the game and put that file back. It's only possible because config files don't get updated until osu! closes properly, which is why crashes always result up in "outdated" favourites.
A helpful tip for those facing such problems.