I have disconnected my battery multiple times while a tune is loaded, and it remains loaded after reconnecting the battery. I don't see an issue.
2003 Redfire V6,
Show: Smoked everything, cobra front bumper, gt rear bumper, rear decklid and lower valence blackout with black mustang letters, 5% rear front 15%, black 98 Cobra rims front, 95 Cobra R rear black with chrome lip, black scoops and spoiler and exhaust tips
Go: CAI, True Duals with flowmaster super 44's, Bama Tune, full suspension (lowered, 8.8, 4.10s, UCA, LCA, springs, CC plates)