They all leave a flash count. However, sommat like Revo, where all their codes are loaded onto the ECU, they just make one flash count. With Bluefin, each time you upload/download to/form the handset, a new flash count is added each time.
Dispite what they may tell you, there is no way round this on modern MED ECUs. Only on the earlier types of ECUs is it possible to disable, or re-write the flash count.