I just thought it was only the E-D that was caught in the loop, and that the Bozemen essentially entered a portal or wormhole that was a single straight-shot to the 24th century. After all, the normal humans of the E-D figured out that they were in the loop, but were slowly suspecting that they might be going a bit crazy in the process (deja vu and the confusion that comes with it), and that was only 16 days. If the Bozeman was in a loop for 100 years
, they would've been extremely frustrated to the point of insanity by the time they escaped, assuming they could detect residual memories the way our heroes did, which could culminate into what Bill Murray experienced in the middle of Groundhog Day before accepting his fate.
However, judging by how calm and collected everyone on the Bozeman was, I doubt that they went through hell.
(On the plus side for the E-D crew, if they die of old age, it'll probably be 16 days later than they were supposed to. Barring further time travel incidents, of course.)