Thanks for the hint @mal, that gave me the information i needed. My problem is solved now, and will share information here in case someone else has the same issue.
TL;DR: I had filesystem errors, used fsck to fix them.
As per your suggestion i started monitoring journalctl -f which showed:
Jul 14 16:08:51 Sailfish estart[13504]: [W] unknown:0 - GStreamer; Unable to pause - "file:///media/sdcard/fc711556-c219-4271-85f6-ecb3fe058b50/Music/Nightwish - Imaginaerum/11 - Last Ride Of The Day - Imaginaerum - Nightwish.mp3"
Jul 14 16:08:51 Sailfish estart[13504]: [W] unknown:0 - Error: "Resource not found."
Jul 14 16:08:51 Sailfish estart[13504]: [W] unknown:0 - GStreamer; Unable to pause - "file:///media/sdcard/fc711556-c219-4271-85f6-ecb3fe058b50/Music/Nightwish - Imaginaerum/11 - Last Ride Of The Day - Imaginaerum - Nightwish.mp3"
Jul 14 16:08:51 Sailfish estart[13504]: [W] unknown:0 - GStreamer; Unable to play - "file:///media/sdcard/fc711556-c219-4271-85f6-ecb3fe058b50/Music/Nightwish - Imaginaerum/11 - Last Ride Of The Day - Imaginaerum - Nightwish.mp3"
Jul 14 16:08:51 Sailfish estart[13504]: [W] unknown:0 - Error: "Resource not found."
This showed a clear hint something is wrong with the file so i checked that out, and found that all the permissions were marked with question marks, like this output (from a different directory):
-rw-r--r-- 1 nemo nemo 6333497 Apr 24 12:08 08 - Sinead - The Unforgiving - Within Temptation.mp3
-????????? ? ? ? ? ? 09 - Lost - The Unforgiving - Within Temptation.mp3
-rw-r--r-- 1 nemo nemo 6156700 Apr 24 12:08 10 - Murder - The Unforgiving - Within Temptation.mp3
Then i found out that the command find . -nouser helped me to find all those files, however the output is a bit unusual:
find: ./Within Temptation - The Unforgiving/09 - Lost - The Unforgiving - Within Temptation.mp3: No such file or directory
find: ./Linkin Park - The Hunting Party/02 - All For Nothing - The Hunting Party CD - Linkin Park.mp3: No such file or directory
find: ./Nightwish - Imaginaerum/11 - Last Ride Of The Day - Imaginaerum - Nightwish.mp3: No such file or directory
find: ./Typisch_Negentig/3-05 - Fiesta (De Los Tamborileros) - Typisch Negentig - Sunclub.mp3: No such file or directory
find: ./Top1000_2015/5-12 - Bad Day - Het beste uit de top 1000 2015 - Daniel Powter.mp3: No such file or directory
find: ./Top1000_2015/2-08 - 'K Heb Je Lief - Het beste uit de top 1000 2015 - Paul de Leeuw.mp3: No such file or directory
Note that these are actually errors instead of the usual file list given by find. These are exactly the files i had problems with, so i tried to delete them so i could copy them again ā¦ but even as root this is impossible.
Then i decided to unmount the card and run fsck:
[root@Sailfish ~]# umount /media/sdcard/fc711556-c219-4271-85f6-ecb3fe058b50/
[root@Sailfish ~]# fsck /dev/mmcblk1p1
fsck from util-linux 2.31
e2fsck 1.43.1 (08-Jun-2016)
/dev/mmcblk1p1 contains a file system with errors, check forced.
Pass 1: Checking inodes, blocks, and sizes
Pass 2: Checking directory structure
Pass 3: Checking directory connectivity
Pass 4: Checking reference counts
Pass 5: Checking group summary information
/dev/mmcblk1p1: 1095/1954064 files (11.1% non-contiguous), 3956874/7814144 blocks
After that i mounted the card again (via the settings gui) and everything was fixed, the files are still there, and i can play them with the media player and set them as ringtone.