If you die any other dimension than overworld, you loose all Soulbound items like your spell book and your spells, or the Drops from the guardians. If the chunk is unloaded where your Essence Generation is standing, all essence in the obelisks and mana batteries gets lost. Batteries seem to get unlinked.
The soulbound bug is a known one. It happens in the majority of pack. Any soulbound items that you have on you when you die in a different dimension, you sadly lose. As for the other bugs, they sound alot like the botania bug as when you go into a different chunk away from the flowers, they get unlinked from the spreaders.
The Problem is not that they are unlinked, but even emptied. had 200k neutral in the battery. Leaving and coming back it had 0.
Hmm I see. I'm sorry, I personally dont know what to do here sorry. But I will tag the rest of @Senior Moderator To get to the solution...
If your on about Botania then its a known matter that they do not save things properly. Best to use Mana Pools instead of Battreys. They seem to work better.
Hmm. Well maybe you can only Produce what you need? I managed to use Ars Magica that way. I never stored anything..
AM2 has the mana empty+unlink bug since they changed to 1.2 version of that and added the new etherium system. Only thing you can do is only create and use what you need at the time of spell creation/essence creation. As for the soulbound bug, make the item called spellbind cloth from either Botania or Thaumcraft and craft the spells that have soulbound on them and make sure to use it on the spell book as well! It will prevent loss on death if you are in a different dimension.
Unfortunately AM2 is super buggy in 1.7. Those that played modsauce know how unusable it was. Unfortunately it didn't got much better. It was quite popular in 1.6 but in 1.7 nearly no one is using it due to the issues. I don't know what else to say besides that is best to not expect anything from this version of the mod.