.trash and super duper

This will be confusing but I will appreciate any advice. The apple genius was not sure he knew the answer so maybe someone here knows what I should do.
I'm not sure it matters how this happened but it started with a failing hard drive and superduper. It's a long story but I ended up with 152 gb of files (all user files, all photos) duplicated on my external drive. I didn't realize this for awhile but when I did, I put all all the duplicates in the trash. Even though .trash files are hidden, they take up space on my external drive plus on my back up drive. I am afraid to empty the trash because I don't understand where the files really are or where the trash is since the only place I see a trash can is in the dock, not on my external drives. I use super duper to clone my mac hd as well as my external drive. I discovered what had happened when I checked the activity monitor and saw that my drives had suddenly lost all that space. Since I can't easily undo emptying the trash and can't experiment with one file, I am really afraid that I can create havoc with the system. Super Duper told me it's a bad idea to keep a lot of files in the trash. I sense that I just don't know enough about this to decide what to do. any help much appreciated.
Thanks.

you can see the hidden trash files. They began with a .Trash
slotless is an external flash drive.
/Volumes/Spotless/.Trash
The user Mac has a hidden trash folder in the home folder.
/Users/mac/.Trash
Macintosh-HD -> Applications -> Utilities -> Terminal
#Show hidden files. All file icons come out dimmed.
defaults write com.apple.finder AppleShowAllFiles TRUE
killall Finder
#Back to normal. Icon are bright. Hidden files are hidden.
defaults write com.apple.finder AppleShowAllFiles FALSE
killall Finder

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