Well he stated using an arduino micro board, which like the leonardo board uses a 32U4 chip, so I don't think his problem is based on the old 'doesn't handle WDT interrupts correctly' problem. I would think all the 32U4 based arduino products handle WDT correctly? And I would not think there are upgraded bootloaders avalible for this chip series anyway?
This sounds more like a problem the very first UNO boards had that if loaded with a sketch that started sending serial data immediatly effected the 8U2 USB serial chip from responding to the bootloader correctly, or something like that? It was fixed with a firmware upgrade to the 8U2, but I recall a work around was holding in the reset button, plug the board in and only release the reset when the upload started?
Lefty