SureAI

I just finished several hours of play and now, when I want to return to Ark, I see that all of my fast-travel scrolls, Ondusi's scrolls (there were a LOT of those!) and other scrolls are just gone from my inventory. My pickaxe also vanished.

Is there a list of console codes I can use to get them back?

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.

They were in my inventory and then they weren't.

It's fine now since I have more money and can replace them, but I'll watch out for that.