If I load a Scene then tweak the sounds when I save the Scene am I also saving changes to the source patches or just the modifications to the source patch? (If I am changing the source patches should I also save the patches with new names?)
A similar question was asked for the Play+ but it seems like there were no replies.
This is true for the Play+ / Tracker+ / Mini and Synth:
Whenever you load a patch, it technically creates a copy of it in your project/scene.
So technically you don’t have to save a a new patch.
But if you want to use them in the future for other projects, you might want to save them as their own patch of course. 
Thank you Sandroid. My main concern was not losing sounds that I wanted to keep. As for saving them with new names as you suggest, as it happens I did that with three patches just before reading this - the first ones I made that I felt were worth keeping.