One type of damage that can happen if the harmonic balancer bolt is loose is that the HB hub wears and the key and keyways in the HB hub and crankshaft nose wallow out. So the HB and crankshaft should be inspected to see if there is damage to the key and keyways as well as fit of the HB hub to the crankshaft nose.
It is interesting that the ECM would pick up the loose HB from the crankshaft postion sensor signel. I am wondering if the HB holds the crankshaft pulse wheel steady on the crankshaft when it is tight. The signel variation may be the result of a wandering loose pulse wheel due to the loose HB. Just a thought.