How to delete local sync

I have a problem. How am I supposed to delete articles when I sync to a folder?

I’m told that to use a program like ProWriting Aid, I should not let them mess with the Scrivener folder, but instead sync to another local folder and work with that.

I write lots of stuff, much of which gets discarded.

When I finally get around to deleting stuff I’m sure I’ll never use, all of it comes back the next time I open the project. I understand that I could have written originally in research and not moved to Draft until it was finalized, but usually I really think I’m going to use the stuff.

Everything I trash comes back the next time I start the program.