Hi,
No problem. With the reset sequence, you might be able to reset it by first triggering a bootloader reset (same as when programming FLASH), and then immediately issuing an “exit bootloader” command or programming an empty image without erasing. Checking the bootloader sources might help find the exact commands or suggest a better idea.
With hardware debugging, if the board has the JTAG or SWD pins exposed, the Olimex debugger should work.
We have also added an option to control the vertical scrollbar in the console to this build: http://sysprogs.com/files/tmp/VisualGDB-5.4.4.2430.msi (under Tools->Options->VisualGDB->General->GUI). The default colors unfortunately would be trickier, so we will try to add an option for them next time we redesign the terminal settings logic, but we won’t be able to add this option in v5.4.