When the Aux system first came out you were able to slot in a dormant gem since it’s treated as r1 while working on upgrading it to replace the current gem. At some point this changed and when a dormant gem is in the aux slot it no longer works.
I just had a thought that with the ‘new’ reso system Lego gems are partially dormant as well and filled with power from the reso gems. Could this be a side effect of that? Because the main gem isn’t fully powered by itself that the aux gem is required to be?
I’m not really sure if this is a bug or just a really odd working as intended. I know a lot of people who did this same thing and gained damage when replacing with a powered gem.