Excellent. I just did something just like this with a 5-gallon batch recently (I hate big batches but it does happen on occasion). I split the primary into two 3-gallon fermenters, then racked both into a common 5-gallon carboy because I needed my 3-gallon carboys back right away for another batch. Worked beautifully.
The key is to try to put your beer into the smallest fermenter that it will fit in, to limit airspace and thus limit chances for oxidation and contamination. If you don't have anything small, fine, but you are at a very slightly increased risk. But it's pretty small.