The 45-year-old Harrington had feared his career could be over after suffering an elbow injury last month, but the world number 169 continued to roll back the years with a round of 68 ahead of next week's British Open at Royal Birkdale.
The three-times major champion successfully defended his Open title there in 2008, the last time the tournament was played at the venue.
World number four Rory McIlroy, who had missed the cut at two of his three previous events, did so again after a 71.
Having picked up three shots on the outward nine, the Northern Irishman suffered a double-bogey at the 13th and ended up one over par, two short of the cut mark.
Knappe, who shot a second-round 65, and Shinkwin improved their prospects of earning one of the three spots in the Open which are still up for grabs.
Finland’s Mikko Ilonen, who held a two-shot lead overnight, dropped down the field after shooting a two-over-par 74, leaving him four behind the leaders.
The top three were one stroke clear of Briton Ian Poulter and Australian Andrew Dodt, with Nicolas Colsaerts of Belgium, world number 10 Rickie Fowler and Gregory Havret of France a further shot behind.
(Reporting by Steve Tongue, editing by Ed Osmond)
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