Actually I just looked and the reason you are only showing 3 photos may be because they've already been removed. So when I first read your question I went into my Photos app to refresh my memory on what to do and to be sure I was giving accurate information. In doing so I deleted some files of my own. Now when I look on the Photos app they are still there, because Photos draws from all sources, but when I go to my device folders they are not there, because the device folders are just that, folders on the device, and do not include any of the cloud stuff. My photo count didn't change when I deleted those photos because it only counts each photo once even though it is in two different places in my techviorment. So you may only have 3 photos left on your phone, which going into the file manager can verify if you don't find any other photos on your SD card.