I was cleaning up on one of my older servers when I realized that there was a lot of stuff in the "sites-available" config folder that wasn't being used, and since everything I needed and rarely modified was in the "sites-enabled" folder, I ran a "rm -rf *" on the "sites-available" folder...
BAD IDEA, it happens that the files in "sites-enabled" were actually symbolic links to the ones in "sites-available", the ones I just deleted.
The good news is that I haven't applied the changes or restarted apache yet, so all my sites are still up. Is there a way to recover these file from the currently running apache process ?
No. I don't think there is a way to get it from the running apache. You have to recover the files from your last backup.
There is "apachectl -S" but I think it checks the new config files for errors only and gives no information about the running process.