I have a dungeon where the player can help one of the NPC's if they choose. This involves running back out of the dungeon with them, but the navmesh bug is preventing the NPC from going anywhere after they go through a load door in the dungeon. I figure I have two options for the release of this mod. (I guess the third would be to redo the dungeon so they don't need to use that zone, but that's too much work.)
I just wanted some opinions on what would be the best way to handle this in my mod. A or B?

A. I can include a readme with instructions that if the NPC stops moving after going through the load door to save, close the game and reload.

B. I can put a script on the NPC that teleports him to outside when he uses the door. The player may be a little confused but the quest should continue without them needing to save/reload.

It sounds like you have an issue different from the NavMesh Bug, as I haven't heard of it affecting interiors... only Vanilla exterior worldSpace. If it IS the Bug, there isn't anything you can do about it currently... you may want to read the on-going discussion which describes it better and has some work-arounds you may be willing to try. The Bug is triggered when Player enters the Bugged cell, then leaves (far enough away to unload the cell's data, such as most uses of fast-travel), then returns again. Upon returning, followers will not enter the area they could when first arriving, unless the console or custom scripting forces them to.

But in my opinion, it sounds like you have a door going to an area which hasn't been finalized, or the doorMarker isn't on a navMesh tri. The tri must turn green after finalizing the area for the door to work correctly. Either that or there may be a missing tri which blocks proper passage to an area... this tends to happen if there are errors detected during the save - then User chooses to delete them (and not replace them afterwards).

It definitely affects interiors, and even Giskard's video demonstration of this proved that much. Though definitely make sure you're finalized everywhere before panicking. It's an easy step to overlook.