I'm not entirely sure what caused it, but after backing up the source for the site and reinstalling Windows, when I went to load my backed up site, the project failed to load, and simply said "System.Runtime.InteropServices.COMException".  There we no errors before backing up, and the backup was simply a copy/paste with no compression, so there was a slim chance of corruption.  Visual Studio still loads, and lists the project, but it's inactive.  Right clicking the project name(not the solution), and clicking "Edit xxx", where xxx is your project name, brings up the XML for the project file.  Doing some digging around in there led me to the "ProjectExtensions" element at the bottom, and in particular the "UseIIS" node.  After setting it to "False" and reloading the project I was back to work.  But the root cause was because I had forgotten to reinstall IIS after my reformat.  Note that just deleting the whole element, works too, but the section is regenerated after the project is reloaded, and sets "UseIIS" to false.

File Expression 0.9.4 is now available to download.  This one is a pretty big update compared to the rest, and addresses some issues that have been hanging around.

File Expression 0.9.4
ADD: Can add a description of the pattern.
ADD: Ability to insert text before or after found match.
ADD: Some logging is now done for troubleshooting failed searches and errors.
FIX: Buttons staying disabled when closing the 'Save File' dialog after a search.
FIX: Issue where selecting pattern action would not be saved.
FIX: Choosing pattern from list where the action is EDIT or ADD does not allow text
 editing until the action box is clicked.
FIX: More tolerant of missing/malformed pattern information.
FIX: Crash when trying to open a file that is already opened and locked.