If you open up the med section directly (vs writing a script) it will take any meds you have as the current list.
ie: I write an Rx for amoxicillin then and close the prescription writer. I look at the med list and see bactrim from last year and decide to delete it. If I open the med list by double clicking and delete bactrim, amox will now show up on the current med list.
Moral, do med reconciliation before you write Rxs.