OP: Yes, your beer will probably be fine if it was for a five gallon batch. The only way to really know is to take a gravity reading and see if it's close to the target gravity range for the recipe.
If you want to ensure that you always have two cases of beer out of each batch, scale your recipes to 5.5 or even 6 gallon batches. I always have beer left over and wind up filling up some small grolsch growlers with the remainder, which is fine with me.
For new styles of beer I haven't tackled yet, or when working with unfamiliar ingredients, i'm taking to brewing 1 gallon batches. That way, if I don't like the recipe or need to work on dialing it in, I can do that without much investment in equipment or ingredients. Then, once it's perfected, I can scale it to a larger batch with a little simple math.