I hope this makes sense? I have beaten the main story and sided with the BOS. Before I got to the "point of no return" I made a save and marked which one it was. That was quite a few hours ago compared to my most recent save. What I want to do now is go back to that "point of no return" save and side with another faction just to try and get all the achievements. Once I get all the achievements I then want to go back to my "main" save which has me sided with the BOS like I originally had. Is this possible? If you go back to an older save what happens to all the saves that came after it?

The quicksaves and autosaves will be overwritten, but any manual saves you make through the menu should be fine as long as you don't save over or delete them.

You can branch your story as you like with manual (hard) saves, just remember which is which.

I'm on a completionist playthrough at the moment and will 'mark' a fixed point before the 3 or 4 endings...

You could always plug in a USB drive and save your files there.

Your original save will be fine, just don't overwrite it, obviously. I did the exact same thing you are talking about and I was fine.