Currently, CH has trouble reconciling a sync if it can't find the right layers. So changing a name or adding/removing something can sometimes mess stuff up. The number of cases where this happens gets smaller with each release - and the next one will be better about this, I've seen it in action - but unfortunately it still happens from time to time.
The mouth and eyes should still remain auto-tagged though - if those aren't, that seems like a bug.
For now, to be safe I would save any heavy rigging until you feel like you're done with the artwork.