While BSM is at 100, desynthing anything with BSM will not lower anything else (you cannot lose skill if you do not gain skill). However, if you just straight-level GSM, you will randomly lose small amounts of BSM skill. To prevent this, you should do the following: BSM > GSM > GSM > GSM > BSM > GSM > GSM > GSM >BSM > (and so on). You can desynth anything with BSM, even level 1 weathered shortswords/daggers (which are the cheapest BSM desynthable items in the game).

Because I'm really lazy, I didn't do this when I leveled my second class. I just leveled it up ignoring the other class, and then when I was done, desynthed like one i90 item and got back all the exp I lost. You really don't lose much, just 0.01 every several desynths.