If you or your ds are worried, next time it happens, rather than the father going up following the chap, so giving him a reason to turn around again, could you wait for a few minutes and then go up - fairly quietly - and see what was happening?
You can always go up quietly because you can say you didn't want to disturb anyone if they were already asleep , likewise make sure that a special toy or book to read at bedtime or something has been left downstairs so you can just be all jolly and say 'look what I've just found downstairs, I know you don't like to go to sleep without it and I want my goodnight cuddle (or whatever) so I thought that I would come and help singleman.'
That way, he won't feel that he has to go downstairs if he is perfectly innocent and just being nice if helping out but you will get a chance to watch if anything seems suspicious.
I know if you think that he is grooming them then this could be construed as putting them in the way of danger but if others are confident that he is ok, then I think the only way to know is to see how he behaves when no other adults are there.
Failing that - any way that a webcam could accidently be left on or a voice recorder to record what's going on so you can look at it later?
shame we have to live in such a suspicious world, he could well be a nice man that has seen his sis or friends struggle with putting kids to bed every night and to do it once in a while is fun and gives the parents a night off so to speak. But he might not be and your son would never forgive himself if he hurt the children so much better to make sure for himself.