There's no way to currently move the save file. Without us making that change, I can't think of a fix for that issue. Terribly sorry about this. I can refund your purchase for the Humble Bundle copy of FTL if you email me at techsupport@ftlgame.com.
@ravenousrhino: Non 1.5.13 save files should not cause a problem. Did you edit it in any way? There were a few save bugs prior to 1.5.13 that wouldn't be fixed by just updating, as the save file itself would be unusable in those situations. You can email me (techsupport@ftlgame.com) the save file if...