So I moved my BTC from my wallet to electrum awhile ago, placed my order and everything went as normal, it was even marked as shipped. My Electrum balance should be 0. I just now accidentally opened electrum and saw that it says all of my funds are still available. I've yet to try to move them around or do anything with them and since I haven't heard of this happening before I figured I'd ask here!
Electrum only polls the server every so often. Sometimes its information is a little out of date. Try closing it and re-opening it, if it's still showing funny stuff, but honestly I would be surprised if this problem persisted for more than a few minutes after you posted this.