Dear Enrico,
It is possible to reprogram those GPIOs by default (upono reset) in Alternate Function, to any other state (input, output or another alternate function) and use them afterward. However you will obviously loose debug functionnality consequently and capacity to reprogram device using them directly.
A simple alternative would be then to connect under reset, assuming reset line can be connected from debug to MCU and reprogram the device after connecting under reset.
Best regards,
Antoine
