Nope, not something you were doing wrong, and a really good question by the way.
Do let us know how you get on. I consider Rolling/4.2 Beta to be considerably better than 4.1 right now. Plus the more users we can get to test the better we can make it.
To avoid the problem of lost data I maintain separate data partitions. To have these automatically mounted you can add these with the OM Calamares installer using Manual Partitioning. Or you can simply add a line to /etc/fstab after installation. Thus I can easily re-install if a break a system.
Post-edit: For all users: As a general rule you don’t want to store any irreplaceable data on a system partition.