OK, I did absolutely zero editing to the interior of Northwatch keep, but somehow a door from in there moved itself into one of my cells. I deleted the door and have tried TesVSnip and regular cleanup to try to get Northwatch to get it's door back, but the door refuses to reload, and Northwatch repeatedly gets flagged as modified in my mod. The first time I save, in every session, I get an error about an "invalid portal" that is being removed.

If you haven't fixed this use FO3Edit to remove the modification. You will get multitudes of errors loading Skyim.esm, but just use delete key to remove the dirty record.

I don't even know what the modification that's causing this IS....I went through TESVSnip repeatly, searching for any reference to Northwatch keep and removing it, but it simply refuses to revert.

Just select your mod in the CK, click on the details tab, use the delete key on Northwatch cell and save. That should revert any changes on that cell from your mod.

Try this on a backup first.

Make a new cell in your esp. Go to your faulty cell and select everything with a drag box. While everything is selected, go to the offending door and click on it while holding Ctrl to un-select it.
Now right click on the active objects that are still selected. Choose dulicate and wait while they're duplicated (can take a while for a lot of objects). When that's done, right click again and select Cut.

Open your newly created cell and right click the void and select Paste in place. Now delete your bad cell and save. Quit the CK, then start it again and load your cell. The offending door should be gone.

Dont forget to show all markers and rooms/portals, or they will be left behind in the faulty cell. Just re-do the navmesh for the new cell.

[Edit]
I also turn off the snap grid, just in case some of the hand placed object jump to the new grid snap.

I actually tried that (even removed ALL cells from my mod by saving them in another one, then copied their contents back with CTRL-C and CTRL-V to new cells) a couple weeks ago...it didn't stop it form happening, unfortunately.

There's a difference between copying and cutting. If there are any errors, you just copy the same errors over to the new cell with Ctrl+C, Ctrl+V. When you Cut, you sever any links with that cell. You will get warnings, and maybe this will give you a hint as to what's causing the problem.

check to see if you have any quest aliases or script objectreference properties pointing to that door (whether on purpose or by accident). aliases and objref properties change persistence for referenced objects, hence the "edit"

however, a "invalid portal" usually happens after deleting a finalized navmesh (the NAVM record is gone from the CELL/WRLD group, but its NVMI record still exists in the NAVI group)

When I stripped all the cells from my mod to try to fix this, I had gotten rid of all the Cell/World groups AND the Navi group. that should have cleared the mod from having any effect on any cells other than the new ones I made to re-import the cell info, but I must have missed something somewhere...