take a look at the a4e releases. They started to re-do their encodes in h264, or publish their current series in both divx 5.2.1 and h264. Additionally, they started re-doing Tenchi Muyo GXP with new subtitles because the ones they used for their first encoding were close-caption subs. A good example is Tenchi Muyo GXP Ep 26 - that one has already been re-done once, so it is currently v2. When a4e finishes their new encoding run, all the encodes with the bad subs will be the v1 ones _except_ ep 26, where it is v1 AND v2, while the good subs will be in all v2 except in ep26, where it will be v3.
Concerning the different codec encodes, there are currently some series that have v2 and v3 published back to back within days. Before, this meant there was an error in the encode, the file is deprecated and removed from the usual anidb display when you open the EP tree - BUT that is now wrong. Both encodes are ok, since one is good DivX and the other is good h264, EXCEPT if there really is an error and one of the files has to be re-done. Then it gets really confusing because we end up with v4, v5 and on and on and on if there are things that maybe need to be fixed in both encodes.
I guess there is a tracker item for this somewhere. I just don't use the tracker. And I posted this before

Maybe someone could give me an update on ideas. I thought about it for a couple of months now and I think the only way to keep things in order is to get "encoding - runs" into AniDB, which could be marked with small logos, like a small "1" and "2" (upto x) which would be added as another small icon to every file, together with the versions.
I know it is getting more and more confusing with this, but you could get rid of the problems with this by just displaying "encoding runs" and the logos IF there really are "runs" for a group for a series, just like the censor logos are used at the moment.