Well that's certainly a challenge.
The first thing you'll want to do is go around the outside edge of your wall and place vertices wherever the navmesh triangles would pass underneath it.
Then go around the inside edge of the wall and do the same.
The result should be a whole bunch of small triangles UNDER the walls. Hold on to those for now.
On the right side of the house (as I'm looking at the pic) start on the right side of the navmesh cell border and begin CAREFULLY deleting triangles until you reach the walls. Then delete the little ones under the walls.
Once you've done that, save your work. Ignore any errors it whines about. Exit the CK. Reload the mod.
Start laying down new triangles in the empty space you just cleared - this will ensure it generates the navmesh form ID correctly so you don't end up with deletions.
For the large section on the left, you should be able to get away with carefully deleting the small triangles under your walls.
Then remove any triangles the house is sitting over - and be careful not to end up breaking the existing navmesh into pieces.
Lay down replacement triangles to cover the parts of the house you can walk on.
Once all that's done, you'll need to finalize the 4 cells the mod is touching so the new borders get recalculated properly.
It sounds like a pain in the ass, but it actually will go pretty quickly once you start working.
When you're done you'll need to run the mod through TES5Edit to clean all the garbage the finalization process is going to create. You're in a highly congested zone near a popular city, so being as squeaky clean as you can will be helpful to yourself and everyone else.