I think the easiest way to confirm is to use a new SD card. Pray that it could solve the problem as otherwise, the phone is the culprit then. Wish you luck!
If you take out the SD card and plug it on another PC or laptop and all files are found still there, then I could say, you have good and bad news. Good that your Sd card is ok, and bad is, your phone is not ok. My honest advise, don't put all the eggs in one basket. All the best to you.
