Upvote:2
As an EU citizen you have a nearly absolute right to enter any EU country. If the immigration officer sees another document in their system they may ask you questions about it, but they can never deny you entry over not being able to show the second passport. Even failure to properly answer a question about the other passport is not grounds for removal. So you can relax and travel with just one passport at all times.
As for why they ask about the second passport - most likely they want to make sure you are who you say you are, so they ask an extra question for verification. I wouldn't worry about it too much.