They actually didn't meet in the '90s in that episode; they were just young adults then.
Since Homer and Marge are supposed to be in the 36-40 range (it fluctuates), there would've been about a decade we didn't see after their high school years before Marge got pregnant and they got married. The episode was supposed to take place somewhere in that time, and was set in the '90s because that's when they would've been in their twenties based on the sliding timeline.
I'm not at all trying to defend the episode, since it was like from 2007 or 2008 and I can guarantee without even lookng that no Simpsons episodes that aired then were good, but yeah. Simpsons is dumb, but it didn't try to blatantly say HAHA THEIR ORIGINAL MEETING NEVER HAPPENED, at least not in that way.
If you want to be cynical you can say the show has always retconned itself each year, as no one ages and things were contradicted even when it was at its peak, so if anything the whole sliding timescale fuckery is in the spirit of the show. Bart and Lisa of 1995 probably wouldn't even remember Christmas 1989, and so on.
The real issue here is the fact that the show's still on the air, which was also the issue about 20 years ago.