Star Trek: 11-ish Times Voyager Lost A Shuttle
2. The Delta Flyer
Presumably not wanting to feel left out, Tom Paris' "hot rod" (thankfully without those dynametric tailfins) took a real beating pretty much every time it left the bay. The Delta Flyer then met its ultimate end by a few Borg torpedoes in Unimatrix Zero. They soon built a brand new one, quicker than you could say "just married" (with cargo containers).
Of course, notorious outlaw Harry Kim — finally fed up with not getting that promotion — along with Chakotay, Tessa, and Captain Geordi La Forge had destroyed the OG Delta Flyer both before and after that point in the alternate 2390 of Star Trek: Voyager's 100th episode Timeless. Whether those events happened or not depends, I suppose, on your version of temporal mechanics.
If Voyager was lost under several layers of ice in Timeless, so were the rest of its shuttles. That musing brings us to our final, most hypothetical, entry.