Is it possible to remove the mods change to navmesh in a given area or outside cell and have the default area from update.esm or skyrim.esm take it back over ?

go to file > data and highlight your plugin file. click on the details button and find the Navmesh edit in the list. If your list of records is very long and you did not assign a unique editor ID, this can be difficult to rummage through. in which case i suggest naming your navmesh something like AAADelete, save and re-open the details window. click on editor ID sort tab to list all records alphabetically. once you find your navmesh, hit the Delete key (you should notice a "I" appear to the left of the name, which is to indicate that the record is now set to be ignored). hit close, and press ok on the data window to re-load your plugin. you can now save and the navmesh will be deleted from your plugin the next time it is loaded in the CK (note only the changes are deleted, and the original navmesh from skyrim or update esm is back)