Deleting back from external drive deleted files from my computer!

Long story short, Ive set up a new computer and am in the process of swapping files from one pc to another. I backed up the original computer (ps#1) on my WD passport and attempted to restore them on the new one (pc #2). I didn’t pay enough attention and chose the option to backup pc#2 instead of restoring pc#1’s backup.
No biggie. Figured out what I did wrong and uninstalled the WD backup software so I could re-install it.
To make it easy on me (hah!) I figured I should just delete the pc#2 backup so I only had one backup to chose from when I did the restore process - So, I deleted the pc#2 restore folder from the WD Backup file folder.
Rebooted the computer, went to reinstall the software and noticed that ALL of my files that I already had on pc#2 are now gone.
I’m assuming that when I deleted the backup files it deleted the original source files as well… What went wrong? (I’m currently running some data recovery tools to try and restore what I lost - and I lost a LOT - but I’d like to prevent this from happening again.)

Hello OliversPS,

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