My supplier sold me a hive with 5.1mm foundation. I hived the ladies and then picked up some 4.9mm frames. At my first hive check I replaced the large cell as much as possible without taking anything they were working on already, with small cell.
My plan is to eventually replace all the large cell with small cell in the brood box.
My question is, is there any reason I can't use the large cell in the honey supers? With, hopefully, little or no brood does the cell size matter?
Absolute not. You can use drone comb in the honey supers.
If you use an excluder (I wouldn't) then it doesn't matter what is in the supers. I used to run drone comb in the supers and it's much easier to extract... but I don't want to risk that the queen ends up in the large comb and lays. So I don't allow any larger cell foundation in my hives at all.