I can assure you I did not take lightly having to reload all websites from backup. Prior to this I checked the "web" folders of all websites and the only thing found was an index.html and an "error" folder. Here
is the link to a trimmed version of the ispconfig_access.log file showing the 404 errors after all the site pages/scripts were deleted. I'm still curious about what scenario may allow this to happen; any ideas?