In my experience, the airline will verify your travel document before you board the plane, to make sure you have it. They will scan the document and (as far as I can tell) send those details to the destination authorities, even if you gave different document details when you checked in online or when you purchased the ticket.
If you nonetheless want to show a different document at the border, speaking generally, it's difficult to say whether that will cause a problem. But for an EU citizen entering an EU country, any problems should be only administrative in nature and should result only in a short delay at most, because the right of entry under EU law could not be curtailed only because of a document switch.
If you wish to minimize the possibility of delay, use the document that you used to board the flight when you clear immigration controls. Do not worry about whether it's the same document you used on an earlier leg, when you booked the ticket, or at any earlier point.