More good ideas here.
The problem with expanse being only 50 LY from Earth is not a big one, if Archer and his crew solve this one in the 22nd Century. By the time of TOS, it's simply a settled issue that doesn't merit mention, as there is no TOS episode that hearkens back to it. By the 24th, it's a historical footnote in the action-packed decades leading up to the founding of the UFP.
I agree that it's not really a problem, I've never been one to complain about prequels introducing new elements not followed up on later. I just thought it was worth commenting on, since a lot of people worry about it.
So let's say the Delphic Expanse expedition is kept because the Xindi/Kzinti pose a threat to Humanity even if the nature of prequels negates it, but we swap out the Temporal Cold War/the Sphere-Builders for the Romulans. What has to change?
Are the Romulans capable of building something like the Spheres? As I understand, some fans debate if they even had warp drive in this era. Can they warp space and create anomalies on a massive scale? Maybe the Spheres are left over from some failed civilization that preceded the Romulans' arrival in the area.
Trellium-D's dual role as toxic to Vulcan physiology and insulation against anomalies becomes more significant. The Romulans might have fled to an area beyond the Expanse precisely because it would give their pursuers a tough time surviving.
The crew of the Enterprise would not be allowed to interact with the Xindi/Kzinti's benefactors to preserve continuity; that means the scripts for Harbinger, Damage, The Forgotten, The Council, Countdown, and Zero Hour would need partial reworks. Harbinger might have to be ditched completely, or just used as an episode to introduce a surviving Sphere-Builder who is unconnected to the larger plot. If the Xindi Council interacts directly with the Romulans, then they probably can't interact with T'Pol. I think it's best if the Romulans only communicate with their clients via subspace, given their habits.
Without the Temporal Cold War, we also end up ditching the episodes Carpenter Street and E^2. There's also the episode Twilight, but that's not a conventional time travel episode and I personally like it, so I'd keep that script and move it to later in the season.