Tron 2.0 states that Master Control was destroyed sometime prior to Feb 1982. With the loss of the MCP, no one at Encom was able to replicate the digitizing technology. Of course, for those of us working with Legacy, the dodge involved would be Flynn still had access, but decided to keep it quiet. Maybe his pattern was stored in there and would be safe, and that he was able to tinker with the algorithms from the inside after seven years of experimenting; possibly with the Isos' help. Maybe he was about to announce that he'd solved that issue and introduce the Isos when Clu decided to take over, and this could be used as a dodge for that Idiot Ball Flynn was carting in regards to why he was making regular trips into cyberspace without anyone else. Going with this theory means his pattern was the only one that could be transported safely.
Per the Ghost in the Machine comic, Flynn went insane and vanished several years after his trip through cyberspace, with no one sure where he is. The main difference is that the last we hear of Flynn is 1999 instead of 1989. So, Legacy compliance means fudging the timeline, but the fact Flynn AND Tron vanish with no one knowing where they went? TOTALLY works in your favor.
The other main thing you have to dodge is Lora's fate. In the Legacy timeline, she was sent to Washington DC for a contract job, and appears alive and well at the Flynn Lives event in San Francisco, still married to Alan and (apparently) happily so. In 2.0's timeline, she was killed in October 1994 when the digitizer misfired. It's implied that she was partly digitized and that what's left of her is Ma3a. Whether this was an accident or if Alan did it deliberately isn't clear. Not like I'd put either option past Mr. Bradley. If you're feeling generous, just use the “our spirit remains in every program” loophole from the movie to explain Ma3a. If you're less than generous...well, I'm sure we can think of something.
Here's the 2.0 trimeline as it appears in-game.
-Master Control has been shut down by this point, and the secret to digitizing anything (or anyone) seems to have been lost with it.
- Flynn comes up with the idea for the Tron arcade game and asks Alan for permission to use the name.
May 1982: Flynn replies back to Alan and Lora's request for parental leave with a note of “you guys didn't waste any time, did you?” (Ah, the marvelous Flynn tact...) And adds that he'd be honored to be the kid's godfather.
December1982: Jethro Eugene Bradley is born. 7 pounds and 8 ounces for anyone playing along at home. Flynn jokes the kid will beat his high score at Space Paranoids within a few months.
October 1983: Flynn gives the green light to a Tron upgrade. There's an email from Alan that indicates Flynn told him everything, and said that was worried about the digitizing tech falling into the wrong hands. Alan found the whole prospect of a human manipulating a computer from the inside “frightening.”
December 1983: Alan's been working on the Tron upgrade, but hasn't implemented it because of a slight problem...With the patch, Tron would go from fighting for the Users to “kill any User that invades the system!” (Clu would probably trade five Isos and Jarvis's left arm for that code. Would have made “Rinzler” much worse).
August 1984: The plan to upgrade Tron gets shelved by Flynn himself, ostensibly to work on restoring the digitizing technology, since the MCP's destruction set them back. Alan's mollified by the chance to be working side-by-side with Lora. Even though Alan uploads the code to the server, Tron himself has curiously gone MIA from Encom's old server. (“Flynn, you sneaky bastard!”)
January 1988: Math Assistant 1 (Ma1a) is implemented. By March, it's capable of recognizing 64 voice commands.
June 1990: Flynn steps down from Encom. Walter Gibbs Jr. Takes his place as Senior Exec VP.
October 1994: Lora Bradly has a fatal accident in the digitizing lab due to a misfiring laser. It's implied that she was partly digitized, and that what was left of her in the system formed the basis of Ma3a (explaining why it is Ms. Morgan's voice under all that distortion).
* A note from Jet's high school indicating he's in trouble for mouthing off to a teacher and sarcastic remarks in the classroom, along with “despondent” behavior.
* A note from the police sergeant saying that Alan left his wallet behind when posting bail for Jet. An in-game flashback indicates that Jet was arrested for hacking into the school's mainframe, ostensibly out of “boredom.”
Feb 1999: Jet's university grades: A in computer science, and 3 classes graded “incomplete.”
October 1999: This is the last we hear from Flynn. It's an email asking how Alan is “holding up.” It appears as though Flynn's working on a screenplay about his memoirs, too. Alan jokes about who they'd cast to play his part. (Ever watch Babylon 5, Mr Bradley?)
May 2002: Thorne is passed up for a promotion to Vice President of Corporate Security. This sets up for why he was greedy and stupid enough to contact Crown and to take Crown's offer.
June 2002: Jet starts working the game division. Judging from the emails, Alan had to talk him into it because Jet needed a co-signer for an apartment lease, and Alan wasn't going to do it unless Jet had a job.
July 2002: Thorne contacts Crown for “freelance work.”
August 2002: Alan announces that with Ma3a's computational ability, the laser may be capable of digitizing organic matter again.
November 2002: Thorne sees Alan run the “orange test” (zapping an orange through the system) and reports it to F-con.
* Walter Gibbs Jr. starts laying groundwork for the merger with F-Con
* J. D. Thorne (Encom's security officer) is approached by to make it a more hostile takeover.
* A gossip email from an “Olivia” to “Nick” says the CFO of Encom is in trouble for misappropriation of funds.
* Alan tries to talk Gibbs Jr. out of selling.
March 2003: The events of the game.
* There is a note in there of Alan trying to contact Flynn using a home address, but there's no indication that Flynn's there to use it.
* A note from “Patrick” (Games department head) to Alan saying that Jet is more than pulling his weight and will be bumped up to lead programmer for their next title.
September or October 2003: The Ghost in the Machine comic