Okay, the good news is that most stuff is working. The bad news is the deletions did what they do best - attach themselves to different assets than what they were intended to refer to when they lost their proper internal reference.
Not such a big deal all in all - that can be fixed with merging and deletion going by screenshots or a side-by-side comparison. You couldn't have properly merged deletions into a master file anyway, manually deleting the superfluous things afterwards would have always been necessary unless you are willing to go the wood hammer route (merge your esp with the master files and then cut out the afflicted cells with TESAME, merge that with a TR_Mainland which has the same cells cut out). The existing changes could be merged in a day or two of effort, which I'm willing to spend.
To compare, I've made several screnshots of the exterior changes. So far I've seen some detailing, some nice detailing, both of which I'm in favor of.
There's also the Daedric ruin which comes out of nowhere, and I'm not keen on merging that.The reduction of mushrooms in the mushroom forest I don't understand - was there going to be something there? The reworked port entrance (sans the giant Sadrith Mora-style gates) looks alright I guess, I would drop the vendor though. The new mushroom assets aren't in Tamriel_Data yet and don't have working textures, so I'd just leave them out for now. If that's okay with everyone I could get to work on that.
If the mushroom forest stays thinned, their shadow spots need to be removed as well. Unless again something else was supposed to go there? Random Daedric ruin is a little odd too, but if there's a reason for it, I'm fine with it.
Removing the new plants is fine, they can easily be added later (once they're in TR_Data) again.
The Daedric ruin was supposed to be almost completely destroyed inside with only a few outlaws camping in the only room that's still accessible. I added it because there is hardly anything to explore in the area.
The cells where I removed some Emperor Parasols was where I last worked on, that's why it looks the way it is. I planned to rework most of it.
Sounds alright to me then (still waiting a bit on this, for further vetos and because I'm admittedly more busy with other stuff than I thought I would be).
As long as it doesn't involve too many doors, it would be easier to just rip those cells out of TR_Mainland.esp and edit them directly, as a mini-section file of sorts. TESAME can sort of do this, or TESFaith. While not really a solution for the cells near Port Telvannis (that would screw with NPCs and doors pretty fierce), I could make an esp for those other ones, with the ruin and the Emperor parasols and the south eastern to eastern island. While I can't save your deletions, I could save further work from being erased the next time we mess with TR_Mainland's assets.
For future reference on WryeMash: this is how one would update dependent plugins after TR_Mainland.esm changes.
After testing this extensively today, I can with some confidence say that it just plain doesn't work.
The method abot outlined does stop duplicate references from spawning a lot of double assets, but the deletion markers still attach themselves to assets theey were not attached to previously. This is already a good bonus, but it's not perfect (but then again, nothing is).
I've attached a tr_ti.esp which went through the process, and a TR_Mainland_Merged.esp which did not is available here - it was merged manually and the duplicates were deleted by what I saw fit. Since it was a proof of concept, I already noticed some interior edits were deleted. If everyone agrees with it, I'll redo TR_Mainland_Merged as the new TR_Mainland.esp after remerging it with the fixed tr_ti.esp. I'm going to script-fix it next.
Otherwise I'll revert to the pre-merge version and we can call this a lesson learned.