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The remakes don't exist in the same way like I said. Sure they pick and choose things to put in the anime to advertise the games (having characters like Lyra and Todd show up, diffrent outfits, whatever is going on with Hisui, etc.), but if Elm discovered eggs in Gen 2, then he still discovered eggs in the anime. The anime pulls from Gen 1 - 8 as a whole and ignores the games's off handed multiverse angle that was set up in ORASThe anime still draws lore and material from the games.
That also still doesn't mean he wasn't researching eggs in the Remake timeline, he just wasn't the first one to discover that pokemon lay them. So who's to say there isn't eggs in ancient times, but he was the first to modernize the research past "oops, all eggs." Because reading through Elm's and Mr. Pokemon's HGSS dialog, it's sounds like he's still knowledgeable about eggs but he had never seen a Togepi egg before due to them being from elsewhere.
Besides the trading post has a Togepi on the banner. It just seems a little suspicious that they'd have the literal poster-mon for pokemon eggs as a logo for a simple trading outpost. I mean it could be nothing, or it could be hinting at something like a breeding side hustle. Maybe you just get random mystery eggs. Maybe you need eggs for research. There's still a lot of unanswered questions with that stand.