I am not too sure what your problem is.
What is the mount point for your external USB drive?
Did you insert and entry in /etc/fstab?
If not, your drive will not be mounted automatically at reboot.
When you install "paquets" (or rather packages) they usually end up in /usr, /bin, /sbin, depending on the package, so I hope that none of the above is sitting on a removable drive; that would be quite an intrepid configuration.
QatQat
If I could have sex each time I reboot my server, I would definitely prefer Windoz over Linux!