My friend the other day was trading in some non found in raid Tushonka's for some AKM's only to realize Prapor the greedy *unt had yanked his found in raid variants and made off laughing.
A word to the wise, your hideout can do the same with things like flash drives or car batteries, both of which you may be saving some found in raid variants of for their respective quests.
One thing I found that helped stop this problem was to place your found in raid variants in a backpack that you move onto your character whilst leaving your non found in raid variants in your stash. This will prevent your found in raid items being used for a hideout upgrade or barter with a trader.
As some constructive feedback for BSG, I would suggest they implement a similar screen on the upgrade and barter screens as with the quest item hand in screen. This is the screen that allows you to select which of the items you want to hand in to the trader/use to upgrade the hideout when making a barter/upgrading a part of the stash.
I hope this helps and apologies if this has already been discussed.