I have a customer with an SX200 EL running Q46.0.10.

A year ago I turned off Save Busy Out Status on his LS trunks because the CO cut a line and when they fixed, I had to go onsite to return his service.

My tech was just out there again and the lines were busied out but we weren't saving the status and there was no trouble with the CO. Besides busying out via Maint is there another way the system would busy out the lines and not return them to service when the trouble is cleared?

In form 13, trunk descriptors, check 'No seize alarm' and 'No Release alarm'.
Also, once the trunk is in a Busy Out condition, the Mitel can't automatically put it back in service. You have to do that manually from the console or maintenance terminal.

No sieze and No Release are checked as well as save busy out status, so what would busy them out and keep them out?
The reason I don't enable Save Busy Out Status is with a PRI, if the telco drops the circuit, the system busies out the ports and if the circuit is returned and Save Busy Out Status is enabled the trunks won't return to service but they will if it is disabled. I will check the docs again but that is how I read it and how it seemed to work in the past.

Save busy out refers to whether the state will remain after reboot.

customer could have busied them from the console? they do have that option!

Your original post mentioned you're having this trouble on LS trunks. They're etirely different from PRI's when it comes to different states of service.