Hi Maria,
Everything depends on the license model you have. FEFLOW Professional and Subscription license allows multiple model runs (operations) with the same model (mesh and problem settings). For example, if you operate with the very same FEM file linked to the FePEST project, this should be possible with the licensing options mentioned. Also, any change you do to the FEM problem, this will not be immediately reflected in the FePEST project.
Cheers
Carlos