From 29" to 25".  Would this affect the operation or reliability of the rifle?

"The M107CQ is 9 inches shorter in overall length (all in the barrel)"
That's quoted from wikithingy.
I shot both versions, but I didn't try to swap uppers, as the CQ was a 107 and the 29" was a 107A1 and they weren't mine to play with.
I have two barrels for my serbu semi and was also considering taking a few inches off of one of them, as the CQ was fun as all fuck and is perfect for concealed carry.

I can't answer your question but, I freaking love my CQ.

You can shorten it, but the flutes will come to an abrupt end at the brake if that bothers you. If you look at any A1 style barrel, the fluting ends about and inch or so before the shoulder.
If you shorten it, the flutes will just end. We did it a lot just experimenting with barrel lengths. It's just cosmetic. If that matters to you at all.

Wish I could remember the name of the outfit in Az or NM that would take your barrel extension and bolt and make you a new custom barrel.

Ken Rasmussen. I believe thats who it was.

I think your definition of perfect for concealed carry and mine are very different.

What about shortening an M82a1 from 29" to
20" ?

Same outcome. Will work, just look a little funky.

I figured they had different parts. Had I known I could just chop the barrel I probably would have kept my 82