The issue is that when Naviate is closed down, it crashes at the end of close down and gives a Fatal Error. This appears on some machines and does not affect the saving of files.
The reason is on some machines the added Naviate commands on right-click context menu is causing the crash.
The solution is to unload the right-click-menu. This can be done with the command (introduced in Naviate 25.3.1) Disable Right Click Menu which is found in Naviate-tab, under Load Naviate. The right-click menu can be set to Always Disabled or Once to load it just during the session.