My take, to make things clearer, is this:
Time passes at the same rate in both universes. 1996 = 1996 an 1 sec = 1 sec.
Wells, when bringing Lois back to her universe, targeted his machine to bring them back at close to the point when they left (leaving a small margin for error).
There's a year between TA? and L&Cs. If 10 secs in the L&C universe = 2 days in the Alt universe, Alt-Clark should have aged considerably (even with super-powers, he ages). They didn't talk about it much, but I never got the impression that it'd been more than a year for him.
The amnesia thing really shouldn't have worked, but in the ep where it was used, Wells made it happen by bringing them back in time to *before* they'd left. In TA? Lois came back to just *after* she'd left. I still suspect that, as in Chaos Unspool, there was something else going on... some kind of hypnosis device or something. I mean, really... if going back in time caused amnesia, Wells's own memory would be (pardon me, Dr. Beckett) swiss cheese.
In any case, TJ, I don't want to say too much, but, although it is a little detail, how it's handled can make a big difference.
Paul
