Relax the comb will get smaller. As as been mentioned a number of times on this forum, when some hives start to go with naturally drawn comb it sometimes results in comb that may appear larger than what is on foundation. As the bee generations pass the combs will get smaller. Just move the larger combs up and use the smaller comb made later in the brood chamber. Over a few years you'll have small cell everywhere. The larger comb can then be used for harvest supers or drone comb.
Given time, everything works out if you let it. Remember: Procrastination is the discission to wait.