I'm not sure if this is a good idea, but you could try control-clicking on Backups.backupdb and choosing "Put Back". BUT if you don't have anything else you want on the external HD, then -- assuming that Backups.backupdb contains only backups, and only things that are already on your computer! -- you might be safer to just erase the external drive and start backups from scratch, to make sure there are no issues with your backups.
The only thing that gives me pause is that you say your website is down because of missing docs. Were the missing docs only in your Backups.backupdb folder?? Normally I'd think that folder would only contain Time Machine backups, which would mean those items were already on your computer....
For additional details, see this conversation with Pondini (a Time Machine expert):
https://discussions.apple.com/thread/4668057?answerId=20790675022#20790675022