Sometimes a young boy's testicles may appear to "shrink" due to hot conditions, this happened alot with my son, now 8 years old. Let your boy go around without pants or underwear a little, especially when sleeping. Examine his testicles every couple days and you should see a difference. You can also try applying petroleum jelly to the scrotum, I do this to my son at least once a week.
Shar,
Once they've descended they won't go back up. They do go up and down on a regular basis. They retract under stress and also if they're cold. They'll hang down if they're warm. Ideal sperm production takes place about one degree less than normal body temperature which is why they're outside the body and this up and down motion helps regulate testicular temperature by pulling them closer or moving them farther from the body. It's called the cremasteric reflex after the muscle that controls it.
In a six year old the testicles are still relatively small and the scrotum hasn't grown yet. That makes it sometimes difficult for you to feel them. Couple this with the normal cremasteric reflex and it's quite normal for them to seem to "disappear." Check him again if you're concerned and you'll probably find them to be normal. It would help if you check them right after he takes a warm bath as they will be hanging lower then.
If you continue to have concerns mention it to your pediatrician at his next visit.