As you are running leJOS OSEK and not leJOS NXJ, I believe the NXT stays in firmware update mode (as leJOS NXJ used to) and the OSEK program runs in RAM.
The firmware running in SAMBA, the boot monitor. There is no change of firmware and no use of lock bits.
As Roger says the limit is much higher than 100. I did several hundred uploads of firmware while I was developing leJOS with no adverse effect.