Boot from SD no longer works, now what?

Already for several weeks I am working happily with my filesystem moved to the SD card. I am using the following fstab entry on the flash:

config mount
        option target        /
        option device        /dev/sda1
        option fstype        ext4
        option options       rw,sync
        option enabled       1
        option enabled_fsck  0

and creating the filesystem on /mnt/sda1 using:

mkdir -p /tmp/cproot
mount --bind / /tmp/cproot
tar -C /tmp/cproot -cvf - . | tar -C /mnt/sda1 -xf -
umount /tmp/cproot

Now as of today, booting with the SD card in does not work correctly. The white LED is on, but I cant ssh to the Yun. Also once, I saw the blue LED (WAN?) flash for a couple of times.

When I boot without the SD card, everything is fine. However, if I then insert the SD card, I can go to /mnt/sda1, but if I do "ls" it is empty? Is this normal?

If I insert the SD card in my PC, I see nothing special. If navigating to /mnt/sda1 I do see files.

Does anyone have an idea how I could debug this, as I cant even connect to the Yun when booting from SD.

note: I haven’t (intentionally) been doing anything related to the Filesystem lately.

note2: I just noticed that it seems my Yun has been reset to Access Point mode when booting from SD (I can see its SSID), although I did NOT press any of the reset buttons for a long time.
I am very puzzled on what is going on…

From power on of the Yun to seeing the Yun SSID takes just less than a minute. So I assume it is not because of the wif-live-or-reset thing that I am in AP mode?