This is Map Pilot AG specific.
There are different parameters that get populated for a Sampling Flight vs a Mapping Flight. You can't create a mission for one and have it work with the other. You could reuse the boundary and create a new flight plan to cover the same area but there are a lot of checks that happen at the time of mission creation that would not be valid for a different mission type.
If that is not what you are asking about we will need to see a few examples. Please email .mme files as part of the support ticket that Sony started.