I may have a heightened sense of risk aversion, but I feel like we need to close the loop on patients. If a patient is active on the chart system, they are "active" in my practice. If they are active in the practice, they need to be followed. If someone has not been in for 3 years, they should have a letter (probably much sooner than that) letting them know they are due for a wellness exam or well-child check. (We try to set people up for their NEXT wellness at each exam every year). If they do not respond, then I inactivate them. What if someone has a problem that you wanted to address in time, but they never came back in? Do you have any record that you reached out to them and tried to follow up? What if they just don't show up for 3 years, but then come down with a breast cancer? There have been court cases lost where the primary doctor did not recommend adequate and timely screening tests for such things.
I'm no lawyer, so ask your own for advice. But, I say you don't want inactive patients sitting active on your books. Ask them to come in. If they do not, tell them you are closing their file and they need to follow up with a primary doctor. I regularly run a search of all patients not seen in the last 3 years and send letters. I deactivate people who leave or who are discharged. If you go into my admin options you will see how many patients are active in my practice. That is very useful for evaluation the health and growth of the practice.
In addition, you HAVE to do this if you are going to do meaningful searches, for instance: a search for all ACTIVE patients with an A1c >8.0. Keep accurate books is one of the keys to having a successfully managed practice.