I will add this as a bug to our list. An exception coming from the filesystem should stop folders.json from being updated with this info. We've seen issues where folders.json wasn't matching what's on disk and we've had issues reproducing this problem. What you described above is an example of how it can become like this. Thank you for pointing this out.
Matt Petty
Senior Software Developer
SmarterTools Inc.
www.smartertools.com