Connect it to a pc and try a scan/repair of the drives "internal" and the sd, may help.
This is exactly what I experience when adding more than 40k tracks to my Pioneer xdp-30r (about 240 Go worth of MP3)
One simple way to know if you're facing the same issue is to browse the folders on your DAP. With only one SD card inserted, the DAP showed me SD1 and SD2 (SD2 was empty).
Only way to allow it to index my music again was to reset it (reset settings or factory reset).
Have a nice day
Thank you both for your help.
I connected the player via usb, deleted all music files from the internal drive , scanned and repaired the internal drive (no errors)
I inserted two new sd cards and put one flac file on each of the internal, sd1 and sd2 cards.
I reset the device to factory settings and rebooted.
On power up I did a full rescan.
The library then showed one file on sd1 and one file on sd2. The internal drive did not show in the folders directory and the file i put on it did not show in the library.
Remounting on the usb/computer showed the file still on the internal drive.
The internal drive shows as 12.4GB I assume the other 3.6GB is allocated to the system.(wish I could see that !)
I still wonder if I'm missing a file on the internal drive. I can't think how to force the system to show/scan that drive for certain.
Any more ideas would be much appreciated.