No, "disabled" does not mean "deleted". They simply will be disabled while you're booted in safe mode. When you restart in normal mode, they will be re-enabled.Does this mean that any fonts I have installed that aren't built into OSX as standard will be wiped off?
You're sure the system fonts haven't been disabled?
Otherwise, it might be a font cache issue. Try clearing the font cache and the restarting.
You can do this using a utility like Onyx, or alternatively run this Terminal command:
sudo atsutil databases -remove
You will need to enter your password. Restart the computer once this has done.
sudo atsutil databases -remove
if its a "work" mac then stop wasting your time and restore the system from your backup that was done before you had a play with parts of the system you clearly do not understand the interactions on your playing