I suspect you'll find that you're mistaken here. If you delete a collection in Zotero, it won't appear in the save popup for the next save.
If you just click the save button again on the same page without reloading, that just reopens the save popup. It's true that that doesn't refresh the collections list, so you'll still see the deleted collection, but that's just because it's just reopening the same pane to let you choose a different collection for the item you already saved. I suppose that would technically be a bug, but it's a pretty minor one that we're unlikely to bother fixing anytime soon.
Upgrade Storage
If you just click the save button again on the same page without reloading, that just reopens the save popup. It's true that that doesn't refresh the collections list, so you'll still see the deleted collection, but that's just because it's just reopening the same pane to let you choose a different collection for the item you already saved. I suppose that would technically be a bug, but it's a pretty minor one that we're unlikely to bother fixing anytime soon.