Too much head space?

Brewed my first batch (an american amber ale) and let it ferment in the primary for two weeks. Tonight I racked it to the secondary and the first issue I noticed is that it appears that I lost a gallon in the process. The second is that I thought that my carboy was a five gallon but looks like it's a six. So, this means that I have four gallons in a six gallon carboy and about a third of the carboy is empty. Is this too much head space? What will this do to the batch?

I wouldn't sweat it too much. Yes, it is too much headspace, but I think most of us have been in a similar situation before and had the beer turn out fine.

Since you moved it to the secondary after only 2 weeks, I am guessing that the fermentation might not be completely 100% finished, combined with the stirring up of the yeast, I would bet that you have created a small blanket of CO2 that is protecting the beer in the secondary. CO2 is heavier than air and it will protect the beer from oxygen, which is what you are trying to avoid (oxidation).

If you have any CO2 at your disposal or maybe some argon (like a spray can for wine bottles), you could shoot a little of it in there just in case, but I bet it will turn out fine, regardless.

On another note, you made no mention of gravity readings. FYI, you are not supposed to move the beer from the primary to secondary until you are at final gravity, which can only be determined from a gravity (hydrometer) reading.

I took a hydrometer reading and it was 1.012. Starting gravity was 1.056. So I assumed it was done fermenting. I'll keep an eye on the airlock and hope for the best. How long should I keep this in the secondary? Is oxidation a quick process or will it have a greater effect the longer it's exposed?

You are in good shape with absolutely nothing to worry about. When you rack you knock the CO2 out of suspension and it blankets the top. Leave it a couple weeks in the secondary to clear and bottle it up. Oxidation is a long process but I doubt you did anything to cause it. A too large of carboy is not going to do it.

Welcome to HBT!

Wow Nurmey! That is good news.
I bought a few 6 gal. Better Bottles meaning to split the difference between 6.5 Gal primary and 5 Gal. secondary. I have since become afraid to use them as secondary. I'm not thrilled with them as primary because the blowoff mechanism is kind of bush league.

Now I will use them as secondary with more confidence. Thanks

Regards.

I've got a few ideas for preventing oxidation with excess headspace - boiled glass marbles (or other sanitary objects that fit), one person suggested a baking soda vinegar rxn and pouring the CO2 evolved into the carboy to displace O2, in the same vein of thought you could swing out and get some dry ice, drop it in water and pour the evolved CO2 down into the carboy - just happened to have some and did this myself.

Don't worry about doing a secondary. Problem solved.