Aside from the obvious (Right clicking in Favorites and choosing Clear Favorites) this is very unusual. When you initially add items into Favorites, they are stored in memory, and do not write the information into the Favorites.DTA file (Located in C:\Program Files\Equis\MetaStock) until you close the program. If the program does not shut down normally (i.e. crashes) any new information added to favorites for that session of MetaStock would be lost.
Items that have been in favorites for several days of closing and reopening the program should not disappear, unless for some odd reason something is damaging the Favorites.DTA file. One thing to start with would be to back up the Favorites.DTA file after making significant additions and compare the file size and make note of anything unusual that may occur when the problem happens again.