I don't know why you experienced those problems.
I have flashed firmware to several drives in an external enclosure (BenQ DW1655, Plextor PX-712A, NEC ND-4551A, NEC ND-3500AG, LiteOn SHW-1635S, LiteOn SHM-165P6S, Sony DW-G120A) and turning off power to the enclosure and turning it back on was all that was required for Windows XP to recognize the drive with the new firmware - no need to reboot.
I also crossflashed a Sony DW-G120A to a LiteOn SHM-165P6S while in an external enclosure and did the same power off/on and the new drive was recognized without having to reboot windows.
Maybe your enclosure is playing tricks on you?
Sorry for the off-topic.