Definitely. They already had two episodes completely ready to go, the entire point in keeping them around and editing them into their new position in the storyline would be to use as much of what they already had as possible. If they were going to rewrite them completely, they'd just have trashed them and made new episodes from scratch.
I think I have the explanation for why it took so long for them to air, too: We know that episodes go into production long before they air - 6 months+. Hence, Rocket VS Plasma was being worked on before Best Wishes even premiered, which is also before Black and White were released.
Back in DP, it took almost 100 episodes for the Galaxy plot to properly start. The reason for this is pretty obvious - the writers knew there was going to be a 3rd version in gen 4 which would feature an altered villain plot, and they didn't want to do too much with the original form of the villain plot until they knew what would happen in this 3rd version. As such, we just got a few episodes to remind us the evil team existed, as the writers stalled until they knew what would happen in Platinum and could write the Galaxy plot proper around that.
They would then repeat this in Best Wishes. We know from interviews that B2W2 wasn't conceptualized until AFTER Black and White had gone on sale, meaning that everything up to at least BW30 was written with no idea of what any further games would do with Plasma. The writers would give them a short intro two-parter in BW23-24 that didn't really concern itself with their game story, and then wait until they knew what the "3rd version" would do with Plasma until they wrote their proper story.
But then BW23-24 got skipped over due to the earthquake. We were told the episodes would be aired at a later date, but not much came from that... so I think the most logical answer is that there were plans to rework (or just outright air) them before too long, but the anime writing staff was given information on B2W2 before this happened, and they decided that since B2W2 featured an entirely different Plasma, it would be more practical to just keep these episodes on hold until B2W2 came out, reanimate the grunts, and use it as part of the storyline adapting the B2W2 Plasma plot, rather than airing them right away mostly as-is, and then having to work around the entire issue with two separate Plasma teams from two separate games.
Makes sense?