I got e new unknown Alien BO. I was doing my free customization, when I got pulled into a Deep Space battle. I lost my design and now I have to recreate it and pay for it.

actually if you cancel before you ok a BO design you won't get charged for it when you visit the tailor to fix it.

Yeah, I've lost some items in the replicator due to those damned deepspace encounters. The only advice I can offer is this: Before you do anything in space, be it officer customization or selling items in the replicator, visit your bridge. That way you don't need to worry about messing up your officers. When you finish just click on the return to tactical view button and you will be right back to where you were. I realize that isn't the best way of doing it, but it's the only real option I can offer right now.

...wow, the bridge actually is useful for something!