One-over for the day and six-under overall, the three-time tour winner was just inside the cut mark with three holes to play before finishing birdie-birdie-birdie on the Lakes Course at Lumine Golf in Tarragona.
The late burst for a 69 lifted Warren, who is involved in the tense event for the first time since 2010, into joint 39th, with two more rounds to go in the battle for 25 cards.
Also still flying the Saltire out of an 11-strong starting contingent are Craig Ross, Duncan Stewart and Connor Syme.
Ross matched Warren’s effort on the Lakes Course to sit joint 47th on eight under, a shot ahead of Stewart after he carded five birdies in a three-under 69 on the Hills Course.
Making the cut has guaranteed both of them a Challenge Tour category for next season along with Syme, who made it through to the final 36 holes with nothing to spare on six under after his 72 on the Lakes layout.
Maintaining an exceptional level of golf, Englishman Daniel Gavins still leads on 20 under, two ahead of Frenchman Clement Sordet. Others in card-winning positions include Sordet’s compatriot Romain Langasque, who won the 2015 Amateur Championship at Carnoustie, and four-time tour winner Marcel Siem from Germany.
However, Italian Matteo Manassero missed the cut, as did Englishman Calum Shinkwin, runner-up to Rafa Cabrerara-Bello in the 2017 Scottish Open at Dundonald Links.