Hello Matías! Welcome to the forum!
This is a known problem. If you import a flightplan from a file and then make any kind of modification to it in the world map such as changing the starting position or any of the procedures, the whole route is re-calculated using the planner built into the simulator. Unfortunately, this is not something we can prevent.
However, there have been a few workarounds! Please see this thread for a potential solution:
Kind Regards,
Malte