One of my employees stole money from me and is now threatening me. What can i do to protect myself and still collect what he stole?

I have a salesman. His main job is to find customers, deliver goods, and receive payment. Recently we had a fallout with him because he was using the company vehicle for personal use. The other day he failed to remit and record a payment from one of our customers, on top of that a number of treys  went missing and are unaccounted for in his delivery. We tried to contact him in order to straighten the situation out however he refused to answer any calls. Today we went to the baranggay to schedule a hearing with him. When he got news that we went to the baranggay he texted us, threatening us that he had documentation that we were an illegal business. We do not have a mayors permit or sanitary permit for our location because we recently moved. We recently finished all requirements with the DTI and we already made visits to obtain our mayors permit, however we were advised to just wait until January dahil sayang daw and pera namin(this is coming from the city hall). We are not trying to avoid paying taxes and we have all documentation from our previous location.
Am i correct in assuming that his threats are irrelevant in his case of stealing money? Also what can i do to protect myself and my company? As much as possible i would like to avoid having to hire a layer because the amount stolen is not that much and i am not financially stable,in fact my employees make more money than me at this point. The point is i have put my heart and soul into trying to build my business properly, and i want to succeed. Any help would be greatly appreciated! Thank You

Those are shallow threats. The barangay would not require your sanitation and mayor's permit if you filed a complain against him. Also, should he want to sue you, he have filed a formal complain against your company at City Health and Mayor's Office. Most of the time also, they City Health and Mayor's office themselves would conduct inspection and not the barangay.

Just tell him that if they proved that you lack the necessary documents, you will only be penalized while if it would be proven that he is guilty of theft, you can be imprisoned.

Thank You! On a side note I am worried that he will go after my customers. What is the best way to protect my business, by January I have already made it a priority to secure said documents. Was it a mistake on my part to not secure the documents a month ago?