If you have an employee on your staff who is in a position to delete checks after they are written, you need to make sure you are watching that bank statement.
Compare the cancelled checks to your system's printed check register and note any discrepancies. If you see a voided check on that register you should be able to find the original copy of that numbered check with VOID marked across its face.
Here's a story about one employee who embezzled more than $500,000 over a period of years from her small business employer using QuickBooks software.