Did it go back in time with the Enterprise? I'm surprised Enterprise didn't attempt to contact them for help when they realized they had traveled back in time. Then again, Daniels did have something to do with it, so perhaps they were sent back the moment they left the aquatic ship?? Just a random thought while netflixing enterprise.
I had the same thoughts, doubts about the plot at this point, thinking about what's going on in the writers heads! The convenience of it all and how can the time travelling Nazi Alien thwarting Enterprise crew's storyline explain or just dismiss the Aquatic's vessel and crew's experience, leaving them out of the equation.
Some points to consider-
Temporal Cold War,
means used to time travel people, and whole ships in all of the Star trekking history,
Subspace corridors & vortices in this series' storyline signifcance
The Xindi's success in utilising these corridors to save time,
Alternate Enterprise E² 117 year mishap with the 11.6 light year subspace corridor,
and Daniels' mission and abilities for the preservation of The Prime Timeline Ultimately being the most important objective.
I've watched Enterprise about 4 times start to finish, and just now after watching the season 3 Zero Hour episode finalé, I decided to delve into this seemingly inconsistent mistake?.. or is it...
It makes sense how Archer was taken back by Daniels in a way consistent with earlier episodes and every other series, like walking through a door, entering a turbo lift, the time portal/The keeper of time.. or Q? but its pre-Q, so no. However the whole ship in most if not all Star Trek series' time travel methods of moving an entire ship to another time/timeline always required a dramatic and more explainable science-driven theory, consistent with all the brand's storylines and series, means of time travelling a ship, requiring something explainable that follows along with all Star Treks time travel theories throughout all the different series, means like using high speed time warps around the sun, Alien influence of warp engines, a time crystal in an actual time machine/suit, these are all very memorable displays of time travel,
But in Enterprise Season 3 episode 21 "E2" we saw how the storyline focused more on the relationship dynamics and the Why more than the how relative to the science after the subspace corridor that caused the alternate generational Enterprise crew threw them back, 117years, ultimately failing twice.
And this crew, still on the same mission while trying stop their younger crew from making their same mistake and focusing on how the relationship between T'pol and Trip would come to flourish.
That particular Enterprise ship made contact, to prevent the original crew from travelling back 117 years in to the past, an unsuccessful attempt At traversing subspace corridors.
These subspace corridors are used successfully all the time by the Xindi, not all of these corridors are the same, the one in "E2" they travel 11.6 lightyears in minutes, the Aquatics got Enterprise back within a day from the vicinity of Sphere 41 but no information on how much distance in light years saved, but definitely less time than it would take to reach Earth from the Delphic Expanse even in a fully operational Aquatics ship, so from that, the only explanation that seems plausible to me is the subspace corridor the Aquatics used to get Enterprise back to Earth was used by Daniels to get Enterprise back to the same time as its captain to continue the plot of the temporal cold war.
As for the Aquatics, well from the undocking and fairwell it makes sense they then jumped to warp to get back to the subspace corridor and back to Xindi territory, leaving no time, ironically, to notice anything wrong with the stars and contact Enterprise.
Even so if the Aquatics got back home to then realise a change in time, communication with Enterprise might still be possible given the communication buoys left deep into the expanse for Earth to Enterprise communication availability.
So I believe Daniels did the same thing, using the subspace corridor, to the Aquatics to get them back to their mean-time, all with the upmost importance to the Prime Time line without anyone but the Enterprise crew their part to play and anyone else for that matter for the sake of secrecy in regards to keeping it out of the time travelling temporal cold War Nazi aliens or any other temporal cold War candidates attentions, therefore off the time travel radar all in order to prevent more incursions, ultimately preserving the Prime Timeline and the Federation.