A player's "best position" is calculated based on his skills, and can change based on training. It might be better called a "suggested position".
How a player performs in a game iis based on his skills, and what position you play him at - not his "best position". How a player trains is also based on the position he plays in your games, and not his "best position".
In BB, players are give a best position of "point guard" if their passing and ball handling skills are higher than their other skills, particularly their shooting skill. This does not mean that they are bad shooters, but instead are good passers as well; or it could mean they a really horrible shooters, and their passing is less horrible. It's mostly relative skills.
You likely trained your "point guard" in jump shots. So now his shooting is better, but his passing is just as good as it ever was. He will perform a little better than before as a point guard (who do need to be able to shoot). If you train outside shooting so that his jump range improves, his classification might change to "shooting guard". And if you were to train passing, he might become a "point guard" again.