There are three different ways I could see this flashback playing out:
1) Young Regina and Young Zelena don’t meet, but their flashbacks parallel one another. Would be the most logical route to go, but this is OUAT, so that means maybe not.
2) Young Regina and Young Zelena meet, but without realizing that they’re sisters.
3) Young Regina and Young Zelena meet, find out that they’re sisters, and then Cora erases their memories of this encounter.
Sadly, I could very much see them going with 2 or 3. The writers can’t help but create contrived flashbacks that just don’t mesh well with the pre-existing canon these days. They like to make their jobs more difficult than they need to be, in favor of “you assumed that events played out so and so, BUT what you don’t know is that this random event also happened!”