Pretty sure the only problem you're likely to get is that ground flax goes rancid quite quickly and needs to be kept in the fridge... if you're doing it in a pepper grinder you might find that you have some whole and some partially cracked flaxseeds left in the chamber, which could go bad.

Depends wether you're talking about keeping it in there all the time or just measuring what you want, putting it in the grinder, grinding, then emptying any leftovers out like you'd do in a coffee grinder.