There may have been a second tea chest* (of the oft-cited "342 chests of tea destroyed") purloined by one of the Sons of Liberty during their politically-motivated 'direct action' (aka The Boston Tea Party) but it was likely lost or forgotten (then disposed of by accident).
Note: the 'second tea chest', gifted to DAR in the late 1960's by a descendant of John Hancock (John Hancock Foster), has since been 'dis-authenticated', even as the BTP Historical Society site (www.boston-tea-party.org) makes it seem as though this chest is authentic. DAR has acknowledged that it is a replica (empty, of course).
One curious fact (confirming this possibility of a second chest) is that The East India Company's report to Parliament (following the Destruction of the Tea on Dec. 16, 1773) lists only '340 chests of tea' being destroyed/lost -- not the 342 chests that have been noted in all historical accounts. If the EIC's report was to document their losses for a future insurance claim (or tax payment exemption), one would think they would have reported ALL 342 chests (listed on the original ships' manifests or the EIC's records). So then, if we assume that this two-tea-chest discrepancy is related to the "two remaining tea chests"...one of these (presumably authentic) chests remains at the BTP Museum; the other of the two COULD still exist, somewhere (perhaps in a private collection, like so many stolen Artworks).
Also, let us not forget that there was a fourth ship containing EIC tea, the William, which ran aground on Cape Cod. The tea was 'received' and transported to a tea merchant's Boston warehouse where it was later destroyed (presumably, by members of the SoL). So, while this batch of tea was not a 'participant' in the BTP, it could have been the source of the second chest (or others), and again, possibly stolen by one of the 'tea raiders' in that later act of tea-related vandalism. But the EIC report (noted above) was no doubt written before this final act of tea destruction, as the EIC would surely have included it amongst its losses (but I am not aware of any further 'lost tea' or other merchandise report, viz a viz the William, reported by the EIC at any subsequent time. I could be wrong there).
But my guess is that it was stolen at the time of the BTP (and why not?) and consumed later (as it was likely a chest of a then popular commercial 'bohea' tea -- a mixture of black and oolong tea's -- from Fujian China, via Canton). But now, consider all the ways a single chest could be lost or damaged in 250 years!