This mod seems to be interfering with my legacy characters that already had themes. One of them seemed to be randomized and another had a normal head again. Is it something I'm missing or does the mod not play well with established legacies, particularly characters that have already dipped into more than one theme?

The mod, as well as Expanded Themes, can change some parts for another, that is done to allow for more combinations. For example Shadow theme eyes will be replaced by shadow wings.

Is there any way to preserve the state of your previously existing legacy characters while using the mod to its fullest going forward?

Sadly no :( You could start a new legacy but you have to begin again, not sure how achievements work then. Any particular Theme you didnt like how characters change? You could remove just that one or two themes that are bodering you from the mod.

I actually really like the mod overall. I have a full shadowed dude who has crow wings and a scorpion tail who loses some if it which is unfortunate. Mod seems like it'd be A+ if you were starting new though. Great work!

I see :( if the shadow character has any other shadow part, he will be able to gain the shadow eyes again in intervals. Maybe i shouldn't change the eyes for the wings in the shadow first part, it was done because lots of themes add new head parts, and they exclude themselves frequently. But i can see the problem when you have another wings :(