Hostility in skip level meeting

I apologize in advance for vague posting, but certain details are intentionally left out due to the customer relationship we have as a contractor.

My company does not ask that I hold skip level meetings with my lower managers direct reports. I choose to do so because I feel it's one of the best ways for me to get a realistic idea as to how the day to day functions, and how I can help improve things.

About a year ago, one of these meetings led to an employee disclosing that he suspects a coworker of being dishonest in how much work he does everyday. His claim is that the other guy does very little work compared to his peers. He sees this person leaving campus for coffee breaks and lunch breaks but still leaves as the end of the alotted shift (instead of working longer to get additional worked hours added to his time card, which is the way it's supposed to be if someone takes an extended lunch).

This is a BIG accusation. The sort of thing that if proven, would be cause for immediate termination. So of course I open an immediate investigation with our ethics and HR team... Only to find... If not nothing... Then, not enough to truly prove the accusation.

The biggest problem is that while most employees are tracked using software the company installs on their computers, these particular employees:

1. Use devices provided by our customer
2. Their duties mostly involve responsibilities that take them away from their desks to assist the customer as need arises

So... The ethics department just...shrugs... And says... "Well... Maybe get badge data??" Not helpful ethics guy. There is no badge data recorded when the employee leaves the building, only when they come back in.

In our most recent conversation, that original employee throws accusations at ME PERSONALLY for doing nothing. I would say he never said any particular phrase that was directly insubordinate, but he was really toeing the line. I told him I can't share the details of the investigation. I told him there are details we are trying to work on to improve the situation. I told him there are levels of bureaucracy that have to be cleared before we can take any formal action.... He just sarcastically said "ok.." And laughed it off.

I will add that there are other elements that I'm not going to go into detail about, as while they may be related, they are not the main subject of the conversation we had, nor the subject I ask to this group. Elements such as, multiple managers over this team coming and going in short amount of time. Nepotism in relation to the customer. Not being selected for a particular promotion. TOO much equity in annual increase. Those sort of things...

So here's my question I have for this community. At what point does general rudeness and disrespect amount to a write up? Like I said, no particular phrase he said would justify a write up in and of itself. But good gracious it felt like I was being roasted.