For a soft foot to result in a 2 LF, it needs to influence the air gap. Otherwise, regardless of the way it is measured or its value, the soft foot by itself will not produce a high 2 LF. The effect depands on the way the structure will deform.
Maintenance staff usually pay attention to what they "see". The base/foundation of a motor, when the motor is removed, is exposed and can be easily inspected for dirt, cracks erosion etc. The lower face of the motor's foot, on the other hand, is not visible except during the removal period (by a crane for instance) unless the maintenance staff pay special attention. At least, this is what I noticed.
After all hold-down bolts were undone and the vibration is low, did you observe the vibration as you tighten the bolts again?
Do you have another identical motor (healthy) next to this, perhaps as a stand-by? Maybe you can swap the motors to eliminate/confirm the possibility of base related issue. It might me less expensive than sending the motor back to the shop for testing /inspection.
Regards- Ali M. Al-Shurafa