I have evolved into doing all of my own medication reconciliation, and with projecting the medication list on a large screen to the patient with the chart open, we go through each medication individually, until our lists match up. This is done usually after going through the vitals, past med, social, family hx, allergies then I either print up a paper copy of the medication list right then or there, or send to the portal, and when I finish my note shortly thereafter the updated med list is captured when I sign off.
However, if I do any e-prescriptions or e-faxes of meds, or delete any meds, I will hold off and then print med list once this ritual is completed.
I have not had the problem with the lists not matching up doing it this way.
But I complete every note as I go before I start the next patient.