Your camera should not be used to store images. You can and WILL lose images some day. It is a best practice to download all of your images to some type of external storage, like a computer.
It is also a best practice to periodically format your memory card in the camera. How often this should be done depends upon how much use you get out of your camera.
Are you saying that somehow your computer is somehow mirroring the contents of your camera's memory card? Any changes on the card are then reflected on the computer when you connect your camera to it?
What computer are you using? What software, if any, are you using for organizing your photos? What specifically do you do to copy photos from your camera's memory card to your computer?
Short answer is.....use the delete button on the camera when viewing each individual picture.
But as Waddizzle says, you shouldn't be using the camera/memory card as a file storage site. Take pictures, then get them off the camera and organize them however you want on your computer.
We need much more details than that. I'll ask again for specifically what you're doing when importing photos from your camera to your computer.
For example, using a card reader attached the computer, Adobe Lightroom is used to import the photos to the computer's built-in storage.
I use the cord that came with the camera, inserted in the USB port. The computer picks that up and then I can download the pictures. I then select the ones for the individual folders I made for them. Then I delete them from the camera and find that those same pictures were deleted from their respective folders.
Do you by chance have the files selected in the camera's File Manager window and in the folder you created both at the same time? If so, when you "delete", both files will be deleted.
Can't imagine any other way your "problem" can be happening.
12/05/2023: New firmware updates are available.
09/26/2023: New firmware updates are available.
08/18/2023: Canon EOS R5 C training series is released.
07/31/2023: New firmware updates are available.
05/18/2023: New firmware updates are available.
03/30/2023: New firmware updates are available.