No worries. I bought a 60L fermenter to do double batches. On one occasion I had a single batch but no free FV, so just ran it into the 60L. It looked pitiful, only filled about a third of the volume, but once fermentation got under way and it got flushed with the CO2, no problems. In fact during the early stages of aerobic yeast activity all that headspace=oxygen could have been a good thing.