Its over.
After I filed the theft report, the Detective calls me and the employee in for an interview. He takes us in separate rooms to talk to us. As the Detective enters my room, he tells me straight up that proving employee theft is very hard to do, even if there is only one guy working at the time. I guess that set the tone for me. Anyway, I went through my whole thing about why I know this guys stole from us, complete with numbers, testimonies, time printouts, yada yada yada. The Detective then goes and talks to the former employee. He is over there for a few mins then calls for me to come in their room. I sit there. The Detective talks to the former employee about all sorts of things. The Detective for the most part, is pushing the point to the employee about how is it going to look to have 'theft' on your record. The Detective says, 'that even if he doesn't pursue theft charges against you, I might'. This goes on for a bit and the former employee agrees to sign a statement saying I can keep is last check, and I sign a statement that says that there will be no theft charges. The Detective sees the former employee out while I wait in the room. When the Detective comes back he tells me that 'It worked out good for you, I didn't think you had much of a case'.
Hmmm... It was interesting to see this play out.