That's why I wrote as far as I know. Steam is pretty stuborn at the moment and doesn't allow me to use the CK.
Wasn't trying to be snarky. Sorry if that's how I came off

Not sure why Steam would be giving you trouble with the CK. Try verifying the tool's contents?
So I've already made a mod that adds a building with an NPC, but I also edited the exterior cell's navmesh to compensate somewhat. Would that mean that the exterior navmesh that I edited would also bug out after moving 2 cells away, or just the interior? The video mentioned converting the esp to esm BEFORE adding any NPCs, so should I delete the NPC I made already (with all his AI data, packages, etc), convert to esm, and do it all over again? :\
Shouldn't matter when the NPC(s) are added and you can't directly edit an ESM with the CK after its flag its master flag is ticked. After all the finalizing is done and all is connected is when you'd want to ESM'ify.
Note: BEFORE editing/finalizing any Skyrim.ESM NavMeshes, give them EditorIDs (NAVM00XXXXXX works well with the FormID as the 00XXXXXX. Doing so will prevent the CK from deleting [00] NAVMs and replacing them with isolated, new replacements native to your plugin.
Note: Before ESM'ification, use the Data > Details window to scan your plugin for any NavMeshes you did not edit and use the Delete key to ignore them. Upon saving/reloading, the 'dirty' [00] ones will be removed. You want to do this before saving your final version so these NAVMs will not be included when NAVI is rebuilt.