If you read the documentation for MolecularDynamics: https://docs.quantumatk.com/manual/Types/MolecularDynamics/MolecularDynamics.html#moleculardynamics-f you'll see that you can pass a previously calculated trajectory as input to the 'configuration' parameter in which case it will continue the calculation. So you can write a script like this:
old_trajectory = nlread('my_trajectory_file.hdf5', MDTrajectory)[-1]
new_trajectory = MolecularDynamics(old_trajectory, <other arguments>)
and it should continue the MD calculation.