On Linux, if a process is holding those file handles open, the OS doesn't really delete them until the process is killed. You can dig into /proc and pull out the file descriptor address, cat the contents back out, and restore whatever is still running as long as you don't kill the process.
For next time Apache is hosting a phantom root dir. ;) These things happen to all of us. We just have to be prepared.
> cd /mnt/backup
> sudo rsync -a --delete user@remote:some/$dir/ $dir/
Only to see the local machine become pretty much empty when $dir was not set.
Funny to still see Apache etc still running in memory despite any related files missing.