When I tried to install a rotating device to make glasses, I messed up the controller settings

I dont think its the machine. I think your settings in Lightburn are not correct.

First thing to do is remove the rotary. And plug the connector back into the Y axis Then go to Laser Tools > Rotary Setup and disable the rotary. On the main screen under “Laser” make sure the Start From: is set to Absolute Coordinates. Then restart the machine and open lightburn and home the machine and see if it homes correctly. 

Remember too
in console you can apply
$RST=*
command to reset your firmware to its defaults if you been changing settings there