Change your mechanic. The cheap (elm327) dongles can't write firmware onto ecus in any setup I am aware of -- elm327 is its own protocol and only supports the obd 2 standard operations (and those poorly). Of course a bad dongle could do something electrical to your ecu, but a reflash would never be necessary. Usually, when your car doesn't start well after a discharge, just remove the source of the drain ( i.e. Don't leave the Doyle plugged in) and go for a nice 30 minute drive -- most likely the battery will be fully recharged.

Why can't they reflash firmware tho? If it give you access to the CAN bus, you should be able to output whatever the heck you want. No?

I recently got a dongle with a power switch; lets me keep it tucked away in the connector without draining power.