The fundamental basis of the entire Rebuilding Your Character chapter in Player’s Handbook II is to allow you to switch from one legal state to another. The very first line in the Retraining section is
The most basic level of character revision is retraining—that is, adjusting a decision you made earlier in your character’s career by selecting a different legal option.
(Player’s Handbook II, pg. 192)
It is a mistake, in my view, to view “legal option” narrowly—some have argued that it only matters if you could have chosen the option at that level and that’s all that matters. I think that is wrong—nothing about the retraining rules suggests that you should ignore the rest of your character. An option is “legal” only if the end result—including “later” developments that are still part of your character—is legal.
(The rules also do recommend not getting hung up on fiddly details of character legality,¹ but I think whether or not you have a psicrystal is not a fiddly detail.)
To wit, if you have a psicrystal, it is not a “legal option” to be without Psicrystal Affinity. You can retrain the feat if you lose or dismiss your psicrystal, but not if you still have it. Dismissing isn’t a normal option for psicrystals (as far as I can tell), but I think it seems reasonable to make “re-absorbing” the personality fragment in the crystal a part of the retraining process.
However, retraining should not be necessary to replace a psicrystal. Psicrystal Affinity’s benefit “allows you to gain a psicrystal.” Nothing about this ability to gain a psicrystal makes any reference to whether or not you’ve previously used it—it doesn’t say it “allows you to gain a psicrystal once.” There’s a lot of implicit suggestions that you can only have one psicrystal—the fact that it’s always spoken of in the singular (many, many things refer to “your psicrystal”), the fact that you have to choose one personality shard for it and it’s not suggested you could then get the others, etc. etc. But all of that is implicit—RAW, you could make a case for not being limited to 1 in the first place. I don’t think any DM would—or should—buy that, but that’s kind of what the rules give us to work with. And while I don’t think a DM would or should allow you to use Psicrystal Affinity repeatedly to get multiple simultaneous crystals, I do think that every DM should allow you to use it to replace a psicrystal.
If a DM does read a “once, ever, even if your psicrystal is lost” limitation into the ability of Psicrystal Affinity, I don’t think retraining it away and retraining it back would “erase” the history of having used that ability, so I don’t think retraining helps matters. The DM just shouldn’t do that.
- Player’s Handbook II, pg. 192:
After your character goes through the retraining or rebuilding process, you might notice that he doesn’t quite match the specs of a similar character built up to the same level by the normal method. Maybe his skill points don’t add up quite right, or his hit points are off a bit from the expected value. But the small variations that crop up in this process don’t significantly impact play balance, and writing rules to eliminate them would complicate the process without really improving the quality of your game.