Yes, I do need to load the AQ32 bootloader back in order to run the AQ32 firmware, however, for the AQ32, it is done through its Configurator which in turn requires a valid COM port to be selected. And that is the problem, the device is not getting detected on the COM port !
I will try out the link that you attached, thanks for that
The board with the AQ32 is the STM32F407. As far as TauLabs recognizing it and working with it, I will be honest and say I do not know the complete details about the inter-working. However, there is a thread on the Aeroquad forum that describes the process to do it. It lists and eq_af32.dfu file which needs to be flashed on the quadcopter. This file contains the TauLabs bootloader, flight code, and data to reset the emulated flash. A link to installing the correct version of the GCS is also there.
Also, the original issue of the PWM Tx/Rx not working with the TauLabs GCS, that issue is fixed. I had to reset the board after choosing the Receiver Type from the Hardware Configuration Tab
Wish me luck as I am just starting and will be all over the forum for more help in the future !