Here is a bit of an odd one.

My wife entered the Schengen zone (at CDG FWIW) with a 3rd country passport, and obtained a new EU country passport while we were in the EU/Schengen (previous one had expired for a few years), and she departed Schengen with her new EU passport. Given that she entered the EU using biometric automated gates, and we will be entering and exiting the EU with a brief overnight stay in a few weeks, should she re-enter Schengen with her EU passport and then depart with her 3rd country passport just to ensure she is recorded as having left the EU? No overstays involved.