Since the last update (current version, MM 0.35.28) repairs of internal components, e.g. weapons are no longer working via auto-/bulk-repair. External armor is fixed and the unit is marked repaired (repair-options are no longer shown either), but the e.g. weapons that were damaged or destroyed are still destroyed and carry over as such to MegaMek.
Manually repairing the damaged slots and repairing ammo after still seems to work.