Hi Nyaru,
Glad we got homing sorted out.
When loading new firmware using the above method, the user settings will remain on the xPRO V5. However, if you issue a $RST=* command, the user settings will be updated to the defaults in the NEW firmware.
So, if you load new firmware and things are behaving strangely, it is recommended to issue a $RST=* command to get the latest defaults, then set your specific settings such as limits, homing, probes, and step/mm. This will really only be needed if we have to change hardware related settings like step_pulse time and we will note it on the firmware release details.