What is the pin state during microcontroller flashing?
I think generally you could consider it a safe assumption that upon reset, all pins will be set as inputs. 

However, even if the datasheet/app notes do not explicitly say this, look at the default values in the pin configuration registers. If your Port direction register resets to 0, and 0 means input, then it is safe to conclude that all pins will be inputs until set otherwise. Sometimes this information is not blatantly obvious. For example, Atmel (8-bit) datasheets tend to put the reset value of a particular register in small text, next to the register diagram.

If you wish to learn more about the flashing/reset process, the documentation is your best bet. My guess is that there exists an app note about downloading code to the microcontroller, probably geared towards setting up a production environment or developing an ICSP. As for reset conditions, that is likely covered in a chapter in the datasheet for the particular model or family of the microcontroller.