Looks like I have solved this problem for myself as follows.
- Resize the existing partition containing markdown notes to 2Gb to keep backups small.
- Move everything else from the
/home/user
directory to a new partition - Mount the 2Gb notes partition on top of the
/home/user
- Create backups of the notes partition using using
ddrescue
It took some work, but ultimately this approach might even be superior as I won’t need to worry about managing the dates in text.