Hmm. You say “We” as in you and at least one other person 
And you joined a PvE server so I’m guessing your main goal would be to build stuff and explore PvE content / dungeons and the likes?
Have you considered either using Co-op mode (for 2 people if you’re constantly together as there is a tether distance) or a simple locally hosted private server if either of you have good internet? (the good internet part is optional if you’re in the same house on the same router as data would go through your local area network)
That way you’d have much more control over the settings and the issues with pretty much anything disappearing would… disappear.
And if some bug still caused them to be wiped, you could simply add them back as the admin.
There’s a thread on here on how to set up a dedicated server app on a windows computer with the help of their launcher to set it up easily, or you could download it from Steam for free and manually edit the config files
The downside would be ofc that the world would be much more empty without other clans and players, however the upside would be full control over your settings and database and even what mods you might want to use.
Just a thought