Actually, if this is part of the S2 Smallville trip Wells took with Clark and Lois, she'll forget everything when Wells drops them back in their own time just before he meets them. Of course, this would give Lois more opportunities to write a note to herself that CK = SM.
If she did recall all of this some time before she figured it out at the end of S2, she might not be so willing to accept Clark's proposal, even conditionally. Maybe he's a dead man either way.
And Morgana's right - this is indeed a cool fic!
