I used the duplicate finder tool. All my Adobe/Art Programs programs are now messed up

I am lucky I had put all of the files in my recycling bin but now I have to wait for 17 hours till all the files are back in place. I did what ccleaners recommended and didn’t click on the one folder to clean out yet here I am with broken apps/programs. What could I have done differently to prevent this but still clean up my PC?