Canon Camera Connect to Iphone to Cloud to Mac Issue
If you have iCloud Photo Library activated, all changes are synced between all connected parties —deleting in one device deletes in all devices. Same will happen if you erased them from your Photo Stream although that would probably leave a copy on your Camera Roll (unless you erased iPhone originals when importing via USB and had only the Photo Stream copy left).

In any case, you can still look for your pictures in the "Recently Deleted" album; manually deleted pictures should be there but I couldn't find the Photo Stream deleted picture on it and I don't know if they are saved there when batch removed after importing via USB.