In a case like this I would take my best guess at a reasonable number of hours and double it. What I have seen in the past is that if a compressor runs wet for more than a few minutes it will die sooner or later. If they just get flooded, never ran and is dehydrated in a few days they are usually ok. You may want to just put replacing the compressors on your bid. Also a few other unwelcome surpises will pop up. If you have to do it, do it on a T&M basis.
The guys are right, you will own this job. A year from now when the same junior engineer decides he needs colder water again, you'll get a call: "ever since you fixed that thing it hasn't been right, and now it shut down". Sell him a new one if you can and tell the Bozo who adjusted the controls to stay away from it.