@SmackAttack86 Please add more info about your system, as requested in https://retropie.org.uk/forum/topic/3/read-this-first.

EDIT: make sure the usbromservice is installed, on a PC is no longer installed automatically, you need to install it first from the optional packages section.

@mitu thanks!

Try running

sudo ~/RetroPie-Setup/retropie_setup.sh

at the prompt or through SSH and then update all packages and see if that puts it back.

Just to add a bit of info, I had this problem and @herb_fargus helped me fix it by telling me to try the enable/disable (which worked well). Thanks @buzz and @herb_fargus!

Link to my post in case there's any useful info there: https://retropie.org.uk/forum/topic/12750/01_retropie_copyroms-seems-broken-won-t-sync-bios-and-configs