My current theory goes like this:
We know that:
- Aura cores are in some way magical, and apparently pretty powerfully so
- There are rogue mages that do experiments on aura cores
- The emperor is power hungry, so he might work with such mages
- Sigrid's aura core is a part of Sigrid
Therefore, I think that the emperor took Sigrid's core and gave it to a mage to experiment on. Then something happened to the core (either the experiment going wrong, or Arkana getting to it to save Sigrid) that caused Sigrid, as Arkana put it, "experience a plane shift".