I use HC-05 as I need master mode. Just replacement for odometer with fuel-usage/etc. It is inside the intrument cluster and it communicates to bluetooth slave on the ECU diagnostics line (pre OBDII).
As it is inside the cluster, I just got a menu item to restart the unit in slave mode.
Once in slave mode the unit waits for serial communication and once it sees something it triggers the watchdog reset.
It is running atmega328 so I have bootloader there.
So one I start uploading with avrdude it triggers the reset, reboots into bootloader with bluetooth still connected reprograms the unit.
No modifications needed for avrdude, I tought about adding a start reset command via serial but as avrdude works straight I left it out.
Basically you could just interface the HC-06 to something with serial line, then use another serial line (HW or software) to retransmit. Just when it first time detects something on input (or implement reset command) you emulate the pin states on DTR/DSR/RTS/CTS to reset/initiate reprogramming.
HC-06 just handles the RX/TX so other commands to the serial interface dont do much.