Okay so after several hours of messing around trying to figure out why my Samsung Galaxy S3 used to play the music I had on my SD Card, but now suddenly did not want to recognize it all, I found a solution.
Backup any music or other data you have on your SD Card.
Using My Files or any other file app (like ES File Explorer) copy one music file (only one) from your external sd card into your device Music folder.
Go to SETTINGS > MORE > STORAGE and choose FORMAT SD CARD. **** WARNING: This will delete everything on your SD Card. Make sure you backed it up before doing this. ****
Once it is formatted, choose UNMOUNT SD CARD.
Once it unmounts, choose MOUNT SD CARD.
Go back to My Files (or ES File Explorer) and copy the device Music folder to the root of your external SD Card. Do not individually copy stuff inside the Music folder, but choose the entire Music folder itself. When you copy the folder to the root of your external SD Card, this means that a new Music folder will appear alongside the Android folder.
Go to music app and you should now see two copies of the one file you copied over in Step 2.
Delete this file from your device Music folder and leave it in your SD Card Music folder.
Go to music app and there should now only be one copy.
Put all your music and data back on the SD Card now, but be careful NOT to copy any hidden files that were on the old SD Card. Only copy over .mp3 files or the specific data files you need.
Hope this helps!