Hmmm, if I were a contractor with any familiarity with such equipment, I would have checked to ensure that power was off prior to ‘messing with speaker cables.’
I would say that if the contractor merely shorted the leads to each other, the damage would definitely have been limited to the amp. If the contractor shorted one or more leads to ground, I would say that there is a very limited chance, and I mean infinitesimal, that some harmful current passed through to the 990. If the contractor shorted one or more leads to mains power, then some current may have passed to the 990, but even if so, almost certainly 99.9% via the shield conductors and case, not likely via sensitive components. If something had adversely affected the 990 as a whole, you would likely have heard the effects through the channels of the amp that continued to function after the damage was done.
While I can’t offer you an iron-clad assurance, from your description I would think that your 990 is in the clear. I would test the 990, once you have an amp to connect to it, using a single input signal on a Y connector. Once all the interconnects are in place and the system is powered up, put the two ends of the Y connector on two of the seven full range 7.1 direct inputs, listen for any difference between the two operating channels. Disconnect one side of the Y only and move it to another one of the 7.1 direct inputs, listen for any differences between the two operating channels. Continue this process until you have compared all seven channels and found the sound to be the same from all of them. After all the outputs are confirmed to be the same, check all available inputs.