Thank you all for your responses! I now realise that having stuff on the SD card might not be a very reliable solution if it is not very stable. Also it would be good to have a certain backup process in place, perhaps to another USB and/or remote location over the network.
In any case, we need to change the installation manual to reflect this knowledge for the installation of Yunohost on the Raspberry Pi 3. This opens up the process of researching and discussing what a simple to install yet longterm stable installation on Raspberry Pi 3 looks like, including external devices and/or automated backup devices and procedures.
I think this needs a new topic. What do you think?
Cheers!