Methods and systems for securing code in a reprogrammable security system are provided and may comprise detecting when a prior version of code is copied over a subsequent version of code. Operations within the system may be controlled based upon detection of the prior version of code. A unique version identifier may be associated with each successive version of code. The system may compare instances of unique version identifier from varied storage mechanisms on a device which may include flash memory, latch memory and one time programmable memory. The same instances of unique version identifier may be compared with a unique version identifier instance independently received from an external entity. When a comparison reveals a prior version of code copied over a subsequent version of code the system may conduct operations specified for a security breach.