Hi Mostafa,
I am not aware of any other suppliers for the pyboard D apart from the micropython store. For the pyboard 1.1 there are knock off versions on ebay, though I've not tested these. Labmaker and OEPS also have some stock of pyboard 1.1s so can still ship breakout boards. I contacted micropython about the shortage back in May and they said they are currently unable to source the microcontroller used on the boards due to supply chain disruptions, and don't know when they will be able to. It might be worth contacting them again to ask if they have any more information now.
Regarding the microcontrollers frying spontaneously - this should definitely not be happening. We are running 20+ pycontrol setups in the lab (using the breakout board 1.2 which uses the pyboard 1.1 microcontroller) and have not had issues with pyboard dieing spontaneously. Your using the 12 port breakout board developed by Andy Lustig right? I've never used those boards and are not super familar with the design so am not sure if there are any specific issues to be aware of with them. What devices do you have plugged into the breakout board? Is it possible that something connected to the board is either delivering a excessive voltage on an input pin or drawing excessive current from an output pin?
Thomas