Eduardo,
I see your question in two parts: R&R and Audit.
You don't do R&R for the auditor. Its the question of how confident you can be about the measurement system - whether is is capable of detecting part variation, special cause of variation etc. This has been discussed several times in the forums. To that extent you should be able to demonstrate that the measurement system has not changed over the last 3 years. (same apparisers, trained appraisers, periodic calibration, no change in methods, no problems with the products checked with this system etc etc). The measurement system usage is another factor. If its used many times every day (eg. calipers, micrometers..) then a period of 3 years between R&R studies does appear to be long.
Audit is conducted against your procedures. What is the R&R frequency as per your procedure? If you have failed to conduct R&R study, then it is an NC. If you don't mention R&R frequency in the procedure, it may be an NC. If the (internal) auditor 'knows' something more than what you are showing him, he can probably make an observation. I am not an expert in auditing, but I'm sure others will chip in with their comments.
Please do a forums search for more inputs on this. Here are a few threads to get you started:
http://Elsmar.com/Forums/showthread.php?t=927
http://Elsmar.com/Forums/showthread.php?t=1073
http://Elsmar.com/Forums/showthread.php?t=3690
-Atul.