I have no special knowledge about the NavMesh updater program. But I have spent a lot of years fixing PC issues.
Have you tried right-clicking on MeshUpdater.exe in the \mq2\release folder and explicitly Running As Administrator?
If that doesn't work here is a troubleshooting/action flow I would take to try and shotgun fix it... (Print this page for easy reference!)
Reverse any changes manually performed to the location and folder structure of MQ2.
If that's not possible reinstall the VV compile of MQ2.
Now, change the properties of the RedGuides Launcher so that it Runs As Administrator.
Run the RedGuides Launcher and ensure the Settings page is filled in correctly. The MacroQuest2 directory MUST point to the correct ..\MQ2\Release folder.
Try the MeshUpdater again.
If it still doesn't work then continue with...
Reboot the PC
Run Windows Updates
Reboot the PC
Run Windows Updates (yeah, repeat this until there are no more Windows updates)
Open a command prompt AS Administrator and paste in this entire following line... (this ensures your Microsoft.Net assemblies are all compiled-up-to date)
c:\windows\microsoft.net\framework\v4.0.30319\ngen.exe executequeueditems
Install the PatchMyPC updater from
https://patchmypc.com/freeupdater/PatchMyPC.exe and let it patch all the non-Windows software...
Reboot the PC
Then install the latest video driver for your card.
Reboot the PC
Then install the DX9 update from
https://www.microsoft.com/en-us/download/details.aspx?id=34429
Reboot the PC
Now, change the properties of the RedGuides Launcher so that it Runs As Administrator.
Run the RedGuides updater and ensure the Settings page is filled in correctly. The MacroQuest2 directory MUST point to the correct ..\MQ2\Release folder.
Try the MeshUpdater again.
If it's still broke you will want to make a backup copy of all your special MQ2 content (INI files mostly).
Delete your appdata for the Redguides Launcher by pasting this into windows explorer search window (any folder) %LocalAppData%\RedGuides and then delete the contents in that folder
Uninstall MQ2 and RedGuides Launcher from the Apps location in Windows Settings.
Open a command prompt AS Administrator and paste in this entire following line... (Schedule the disk test for the next reboot!)
chkdsk c: /f
Reboot the PC (let it run the disk test, it only takes a few minutes)
Use Windows Explorer and delete your MQ2 installation folder (you did save a copy of all your INI files right?)
Download and reinstall the current RedGuides launcher. (Reconfigure macroquest.ini based on your saved copy.)
Copy any custom INI files from your saved backup.
Try the MeshUpdater again.
If it still doesn't work there are larger underlying issues with your PC.