I’ve been having this issue too the last two days and I’m in the hole about $600 now with over 27 packages affected. When talking to support I just get a lot of “it’s a known issue that’s being worked on” but no estimate of when it will be solved, or when/if I will get refunded. 
I’m really surprised this hasn’t been resolved yet, this is a lot of money that merchants are losing from this weird glitch. It not getting immediately resolved is honestly making me lose trust in shopify tho.