This is the easiest way to do it, but make sure you select "Only update this game when I launch it" before making the appmanifest file Read Only as that file is where it saves that info to.
Edit:
Here's updated steps
1: rename Fallout4 folder from \steamapps\common\Fallout 4 to "Fallout 4 - old"
2: rename \Documents\My Games\Fallout 4 to "Fallout 4 - old"
3: reinstall Fallout 4
4: open steam and right click Fallout 4 > Properties > Updates > Automatic Updates:
"Only update this game when I launch it"
5: set the \steamapps\appmanifest_377160.acf file to read-only
6: name new Fallout 4 folders in common and My Games to "Fallout 4 - new"
7: copy and paste "Fallout 4 - old" in common and My Games so it makes a copy
8. rename the "Fallout 4 - old" folders in common and My Games to "Fallout 4" so steam recognizes them
9: continue playing as if nothing changed (this might only work if launching from F4SE?)
Now you should have a regular one, a "new" one, and an "old" one that's a copy incase anything breaks.