I have a misdemeanor theft, I was late for my first "court" appearance, the front desk said to come back, meet with them and the warrant will be gone?

Most court's have a process that allows a person who missed a court date to get back on the docket by showing up in Court on a certain day and time (maybe in the court you are in they do that Monday through Thursday).  At that time it is typical that the court 'quashes' the warrant (you are not arrested) and gets the case back on track, which often invovles talking to the prosecutor to see what resolution can be reached.  So it sounds like they have that process.