OP, you want opinions, and mine is that you are making this a far bigger deal than it really is. Classes are split all the time in primary schools - its very common, happened to me twice. Did you expect them to stay in the same class forever, and on to college together too?!? Yes, your son is in one class and two friends in another. Next year it might change again.
When I was younger, we moved a lot as my family grew. I clocked up 4 different primary schools in total. With each new school I went to, I lost my existing friends and had to start all over again. First day of school was met with anxiety but I always got through it. I now have a few different groups of friends, but I can honestly say none of my close friends are from primary school - its all from 1st year onwards. That might be in part because we moved so much but it hasn't done me any harm! In fact, I reckon its part of why I am so sociable, having to make new friends. I was a bit of a target, big glasses, awkward etc. so yeah, I reckon it helped.
There are only a few things you as a parent can really do:
1 - Talk to principal re: notification going forward. (Remember that even if you had been told, theres still nothing you could have changed about it).
2 - Explain to your son that as he gets older and goes into new years, he won't always have the same people in his class - and highlight this is a good thing because he will make more and more friends and get to know everyone. Explain he will still see the other two at activities etc.
3 - On first day back at school, have a quick word with his new teacher, explain his anxieties (and yours), and ask her to sit him with someone who is friendly.
At the end of the day, he will be fine. This is a life lesson for him, it will not scar him as you fear. You can't shelter him from this unfortunately.