I had to reinstall Neon because some update (not sure which) broke grub. I let Neon re-use the old root partition for the new install (I did not manually partition) and checked the checkbox that said "reuse the other partition for home". When I logged in, I found that the existing .config and .local folders for this user had disappeared. I looked for backups, but there don't seem to be any. Since everything else is synchronized to other machines, that was quite a loss... It contained, for instance, my akregator feed with more than a hundred rss feeds.
Sorry about that. We use Calamares so I'll just pass this onto the Calamares dev. I've been complaining for some time that it should make it easier to reinstall over a single partition (how my computer is set up) without wiping /home. Is this the same issue or a separate one do you think? https://github.com/calamares/calamares/issues/1878
It sounds a bit related -- I didn't check the Documents folder (which is a symlink into a dropbox folder for me...).