BRUSSELS, Aug. 29 -- For most of this summer, the thing standing between a Schengen arrivals hall and a four-hour queue has been a clause. Regulation (EU) 2025/1534 lets a border post stop capturing fingerprints and facial images for up to six hours at a stretch when waiting times become unmanageable, while still recording digitally who entered and who left. Guards at Paris Charles de Gaulle, Amsterdam Schiphol and Lisbon have reached for it repeatedly since spring. On September 6, it runs out.

Frontex has confirmed the flexibility will not be renewed. That decision was taken over the objections of nine national governments and of the entire European aviation industry, and it is probably the most consequential thing happening to European...