@piyush, As far as I know they cannot penalise you for the past. And without your telling them how are they going to know that you were using Windows in the past.
We had such a auditing in our firm. it went fine. They came and checked a few systems and ensured that it was using Linux only, also they were seemingly surprised to know that we were even using our printer over the network in Linux. In summary the auditing went fine, and there were no problems at all. From my personal experience I feel that you're worrying unnecessarily. Just allow them to do their work, and they'll be off in no time. that way you can also be at peace.
N.B: I'm basing this opinion on my experience and knowledge. Its better for you to consult some experienced linux system administrator to know the real scenario.