Not 100% on this, but based off of Roy's instructions on converting mods, it looks like plugins with Navmeshes just need to have all their Navmesh edits refinalized in GECK, then made into an ESM since NV doesn't like having Navmeshes in ESP plugins. Currently trying it out on my build.
Just got done testing it briefly. The GECK crashed a couple times from finalizing all those Navmeshes in one attempt (save every change in Y axis, then quit to fix that). I couldn't see any real issues besides frame drops due to a heavy amount of new items. One note, companions can't figure out how to climb the ramp to the roof of Super Duper Mart. I don't know how to edit Navmeshes so I can't fix that, but finalizing all the new ones added from this mod (easy to check in xEdit) seems to make it work.
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Just got done testing it briefly. The GECK crashed a couple times from finalizing all those Navmeshes in one attempt (save every change in Y axis, then quit to fix that). I couldn't see any real issues besides frame drops due to a heavy amount of new items. One note, companions can't figure out how to climb the ramp to the roof of Super Duper Mart. I don't know how to edit Navmeshes so I can't fix that, but finalizing all the new ones added from this mod (easy to check in xEdit) seems to make it work.
-IAreBob