The runaway child will remain in the system as a Missing Person until she is removed by law enforcement. In theory, she will remain in there forever.
If she returns home, notify law enforcement. They will either take your word for it and remove her from the system, or, they will have an officer respond to verify it. Practices and policies vary by agency.
Do you think her mother might have reported to the sheriffs department that your daughter is safe, so the missing child report has been "unreported" or closed, or could the State be housing her temporarily? Or does the sheriffs department still have your daughter listed as missing?
Have you had any contact with her at all since she ran away?
Keep in mind that if the child is with another parent - even if in violation of a visitation order - the child is not generally going to still be "missing." There may be another issue involved, but the child would not be missing any longer.