I'm not quiet sure if I'm the first person to discover this, because I havent heard of anybody else using it, (I bet I'm not)
Say you have a fairing, and you finish it, and it pops up with a message saying "warning: cannot accept current changes. Fairing is colliding with invalid assembly part." So you try and try and try! To get the fairing right, but one of the two keeps happening;
1. You can't do anything without the fairing saying the message
or
2. You can get a fairing, but it is not to you're liking
Well, I have a easy fix for you!
So, I discovered this while playing around, but it turns out, all you have to do it get the pop up message, and after that you can do one of the two things;
1. Click on any place, then place it back
or If you don't want to replace a part on the craft
2. Click on any part on the part picker and recycle it
It's literally as simple as that, hopes this helps!