It is still happening - but I just found a way to "fix" it...
for me, not only were the dropbox folders disappearing from ios file "favorites" - when long press the folder in dropbox (or in file manager) the folder appeared to still be marked as a favorite - and I could not UNfavorite it.
Anyway - instead I just dragged the folder back over the Faviorites section - and it appeared.
so - problem "solved" or at least worked-around.