Clean slate scrolls

Are there any limitations on them?

Cant be used on cash items, even the perma pet rings iirc. Some (the most common ones) can boom your item.

Can they be used on items that have been equip enhanced?

If the item had a scroll fail on it, yes. Remember enhances can only be used when an item has 0 slots available.

Could I fail multiple scroll slots now and still recover all of them months later with clean slate scrolls I don't yet own?

If there's another even in the future for them, yes.
Would I advise it since there's no guarantee you an farm them? No.