I have a 5 gallon glass carboy that I use for a secondary when making 5 gallon batches. I would love to get two batches of beer going at a time and I have a 6 gallon carboy that I've used for wine. Would it be okay to use the 6 gallon as a secondary? I know by that point the yeast aren't producing CO2 as vigorously, so I'm unsure whether I need to be concerned about the excess head space.
I've done it and it works fine, although it isn't ideal. You do risk possible oxidation, but if you don't keep it there for too long you should be OK. Do you happen to have a CO2 tank to purge the 6 gal. with? Or how about using the 6 gal. for the new batch of beer and skipping secondary on the other one? Secondary is usually unnecessary.