Star Trek: 11-ish Times Voyager Lost A Shuttle

Properly speaking, this entry doesn't count as a loss, but as a charitable gift of two Class 2s to those in need. Furthermore, given one extremely heart-warming scene in Star Trek: Prodigy (I'm not crying, my ocular implant is malfunctioning!), it may have turned into more of an extended loan where Starfleet was concerned. Nonetheless, Voyager was still down two shuttles at the time.

Captain Janeway and crew's defiance of the anti-telepath Devore regime in Counterpoint was a masterclass in standing up to xenophobic bullies with bigger ships. Thanks to Voyager, the Brenari refugees make it triumphantly into the wormhole to safety, clear of the persecution they faced in Devore space.

Nine years later, at least one of those Brenari refugees had gone on to serve in Starfleet, aboard the USS Dauntless no less, this time coming to the rescue of Admiral Janeway. If the Brenari came to Starfleet, perhaps those two Class 2s did also and now take pride of place in the Voyager/fleet museum.