Hello Jerome,
unfortunately, I do not have enough information, so I do not have any idea, what could be wrong.
I can recommend you some general points.
If your bootloader runs the application directly without microcontroller reset, please ensure that bootloader cleans up all resources which it used.
Also, you did not explain the behavior. Does it mean that bootloader does not run the application at all, or application does not run correct, or...?
Please write me back as much details as possible.
Regards,
Martin