In the scene where Flynn is talking to his friends in his apartment above the game place, notice that he is wearing Nike sneakers.

In the scene where the laser starts to deconstruct him, notice that he is now wearing Adidas sneakers.

It doesn't make sense that Flynn would change his Nike sneakers to a similar type of shoe when they decide to enter Encom h.q. If a group of computer hackers are about ready to hack, break-in or crack some system, they would so passionately involved with their plan that it would be very unlikely that someone would want to change his/her shoes, especially if the shoes are of a similar type.