IMHO the story holds together very well at every possible level, leaving open just enough questions to allow for interpretations that satisfy everybody. Apparently not, though.
Anyway...
1) The E-D is caught in a loop about a day long. It does not follow that the
Bozeman would be caught in a loop of that length. The
Bozeman is only looping in the 24th century, where she is within the influence of the (spatially quite limited) anomaly that resets the clock whenever the E-D blows up. She only arrives to that location and time
once.
2) We don't know exactly how many loops the E-D went through, but we know she spent only 17.4 days in total in those loops, as counted by "outside observers" (a timekeeping net outside the influence of the Typhon Expanse anomaly - compare to #1 for why the
Bozeman would
not be looping in the 23rd century). So the odds for noticing the deja vu phenomena aren't incredibly low or anything - you are cued in after less than a dozen loops. That is, assuming the loops are a day long and allow you to fumble with glasses of water and whatnot. They weren't that long for the
Bozeman.
Other odds and ends:
3) The dozen or so loops would appear to result in a dozen or so timelines, most of which feature debris from the lost E-D plus a rather shaken
Bozeman. A fun thought, that. But shouldn't there be a dozen shaken
Bozemen now? Well, no, unless the
Bozeman managed to fly outside the spatial reach of the looping phenomenon (to the "safe zone" where the timebase clocks keep happily ticking) while the E-D was busy exploding. And we have no reason to think she would have. The loop clears out the debris and the leftover starship.
4) The decision not to alter course makes good sense in this episode, unlike in "Time Squared". In that earlier episode, the course of the ship was known in advance: she was traveling from A to B. If this was to lead to a disaster in the future, it would be logical to take a detour to C. However, in the episode at hand, the heroes were idly exploring, which involves taking random turns and poking at assorted things. Nothing about this would be known in advance, so the heroes
- wouldn't have a yardstick of what not to do, and
- would realize that the loop they are caught in is a robust one, since it caught them during random unpredictable action and then did this again several times before the heroes knew to be wary of their random unpredictable actions.
5) The collision is a weird one. Is the tractor beam on or not? Why does a collision of two nacelles blow up one ship but not the other? How could the shuttlebay air suffice in moving the E-D, and how would that movement (forward, perhaps with a pitch down meaning the nacelles come up) protect her from the impact we see? All this is details, though - and the loop was a robust one, perhaps exactly because the collision was an inevitable one somehow. Say, the approaching of the E-D would always trigger the century-long time jump gateway exactly at the right spot relative to the E-D to create the collision ("dead ahead" ought to suffice and is natural enough). We don't have any reason to think that the time jump of the
Bozeman would happen without the E-D being there to trigger it, after all.
Timo Saloniemi