The console won't help you find your exact items because it doesn't know what's missing.
Where do your items disappear, in the normal inventory or in the safe chest or loosely deposited?
Otherwise, stolen items will disappear from your inventory if you are caught and pay a fine, for example.
(Scrolls are consumables that are gone after use).
Your current game was started with ForgottenStorys and not with the old previous version?
Have you ever repaired your
installation with Steam?
Have you installed any mods that change anything about this? This is possible if these mods are installed or uninstalled.
Maybe, Savegames might tell us what happened, once before the problem and once after.
You can find the savegames under: C:\Users...\Documents\my games\Enderal
we need the *.ess and the *.skse file, pack both to a zip/rar/whatever archive since the forum doesn't accept *.skse.