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Click settings in navmesh generator and make sure the path is set to the right folder.
I have multiple installs. Was my thought. Have you saved the mesh before?
Are you clicking the save button at the top left after saving the stuff on the right side. Also not sure which mesh files you are editing but some zones have crystalcaverns and crystalcavernstwo. Also, tried running mesh generator as admin.
I figured out my issue. New PC had OneDrive installed on it and it was putting copies of MQ2,Nav,etc.. all in there. I removed it all and reinstalled MQ2Nav. It worked perfectly, except it created a new folder in MQ2Nav called "MQ2Nav". I just have to drag the edited zone mesh from there and drop it into the previous folder.