Thanks for sharing the details about this.
I've uncovered a mapping problem that can cause code coverage instability and code coverage loss in a similar way to what you describe. It occurs when an unopen code file is changed on disk before more work is done (and tests are run) using NCrunch in the IDE. This could happen as the result of a VCS action, or by a refactoring operation (i.e. 'Rename'). A fix is being prepared for the 1.45 maintenance release due out in a few weeks time.
What I'm curious about is whether the issue you've experienced is a result of the above, or if it's another mapping problem entirely. One way we can tell is by checking for NCrunch log file exceptions when you notice the code coverage is out of alignment. When this next happens to you, can you submit a bug report with a link back to this forum post in the description? I'll then see if there is a clear indication of whether the problem has been solved, or whether this is a new one!
Cheers,
Remco