So the issue started when thunderbird tried to compact emails but failed and prompted that not enough disk space. That was weird message since my linux mint is installed on 64GB ssd. So I did a disk usage analysis and found that my home directory is accounted twice. Once in media/... and the other time just as home
The disk usage for both is 12.2GB, out of which 7.5GB is thunderbird. So it seems that 7.5GB of my emails are stored twice.
Anybody know why this is? How to get it so that my stuff would be stored only once?