Custom difficulty part sounds like new version new save issue
Particular with you saying this is one of your favorite games, I would assume you've played older versions and have older saves
(Below is repeated info)
(Apologies, this is going to be reposted info quite a bit of times)
you can either
A) check the stickied "FAQ 0.1.1"
B) check the confirmed bug list ported from discord (paraphrased, should have confirm and discord in the title though) (on here)
C) Get on the discord and check #confirmed-bugs under "new version, new save"
D) https://discordapp.com/channels/285355434741858306/285595458750119937/5819297630... (this is a lcomment link, of an image/comment I posted for the location, as well)
E) Alternative workaround (not a fix in the slightest) Change what difficulty you're playing on. (this will most of the time, work, As its usually your old saves that are causing the issue, and unless you have saves of every difficulty, it will avoid creating the conflict when you choose a new save difficulty that you didn't have previously)
If you still have issue past that, feel free to tell me (you can get faster results over discord)
the save reload... I would want to see the savefile for before I could say for sure... It vaguely sounds like a few things, but some of it stands out
Shields part is at least known, it's being worked on...
The customer - a save reload normally would fix, but in your situation, during gameplay, using the furnace might be an option, since it can delete most things in the current public version... it would probably work... probably... (not tested)
Ore veins
All ore veins start as stone on a fresh save/new player - anytime "new player" bug occurs, it'll be stone again (along side all the duplications that occur)
Your two options here are either wait around for the "Depleted vein" to kick in and recycle them, or, save and reload - which would end up forcing them to unload and reload, usually resulting in various ores - Non-depleted vein recycle time is shorter (usually occurs at midnight/turn of the new day), depleted vein is longer, though I can't swear to how long
I've had reports of people waiting and getting veins, even though I myself wouldn't be that patient.