Once your restaurant reservations are made, they're made. Nothing you do to your resort reservation will change them.
You also don't have to make restaurant reservations "under the free dining plan" as your previously made reservations will not change at all.
At the reservation stage it is irrelevant as to whether you have a dining plan or not, much less whether it was free. The only exception is making a reservation at CRT or a dinner show without paying in full at booking; you must have a dining plan attached to do that. If you have a reservation at CRT or a dinner show that you have already paid for, try calling Disney Dining and ask about switching that reservation to the dining plan so you can get a refund. There are reports that sometimes that works. Sometimes it doesn't, so you can also get a refund when you arrive at WDW.