Well, I'm still in trouble. It wasn't the filesystem, apparently.
After having flashed at least twenty times the emmc, it still refuses to use maps offline. Now I've moved away the whole /home/user/MyDocs/cities branch and the .qf file, and tried to start over by rerunning maps, but the directories are not created again. I'm seeing map tiles get cached under /tmp but of course this disappears when the device is off.