In what didn't make it into the final movie but is in the script, one part of the fans' competing theories is that the brain of the person who activates the Omega 13 isn't affected.
As you know I strenuously disagree with this theory, Brandon. if
all molecules were rearranged, then everyone would be back in
time 13 seconds rendering the device useless.
No because the brain of the person who triggers the Omega 13 is
not affected, so THAT person still has his memory after the time
jump. And everything is as it was, a chance to redeem a single
mistake or misstep.
Thank you, Katelyn. Excellent.
You're welcome, Brandon.
(Source linked above.)
In the final movie, Brandon explains his theory that it's a matter rearranger. Gwen wonders what the use of only 13 seconds is, and Jason replies that 13 seconds is enough to correct a single mistake. The issue of remembering or not isn't brought up. Presumably this was simplified for the purposes of pacing, leading to the minor hole you bring up.