Wilkinson opened with rounds of 71 (stadium) and 73 (Nicklaus tournament course) to slip to a share of 110th after two rounds.
The former PGA Tour professional, who finished 59th on the web.com Tour money list, made three birdies but two double bogeys on day two as he finished on an even par total 13 shots behind leader Meen Whee Kim.
Lee's chances of returning the PGA Tour in 2013 have also faded.
The 21-year-old, who finished 159th on the PGA Tour money list to lose his card, added a three-over 75 to his opening round of 72 and fell more than 30 places on the leaderboard to be tied for 150th.
There are six rounds in the qualifying event with 172 players competing for only 25 places on the PGA Tour in 2013.
Wilkinson is seven shots off the qualifying mark and Lee is 10 shots back from finishing inside the top 25.
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