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I use custom mp3 files to ringtone and notifications. But after a reboot, these settings return to their defaults. Ringtone choose from a music library. Notification is mp3 file in the /sdcard/Notifications/.
Sound notifications setting in other applications (such as Facebook) do not change after a system reboot.
Tell me if issue is the same if you store mp3s used for ringtones in the internal storage
Mountpoint /sdcard/ is internal storage. Folder name '/sdcard' is for compatibility reason. True SD card is in /mnt/ext_card. As I wrote earlier all mp3 files are in /sdcard/Notification and /sdcard/Music.