Organizations are all about protecting their young arms. They heavily monitor pitch counts and usually set an innings limit so that there is less chance of them over working their prized arms.
Joba Chamberlain is considered to be a future No. 1 starter for the Yankees, which is why the team has been so careful with him. He went from being a starter in the minors to a reliever, to limit the number of innings he was throwing.
The following season, Chamberlain was being stretched out in the bullpen to be converted back to a starter. By going about it in that manner, Chamberlain's innings total wasn't as high as if he had started the season in the rotation.
Despite their best efforts not to overwork Joba, he ended up on the DL last August with a tired shoulder. Maybe he really wasn't cut out to throw 200 plus innings in a season?
Chamberlain started the 2009 season in the starting rotation, and for the majority of his starts, he hasn't lasted past the fifth inning. As a result, his innings total is not as high as it would have been if he had been able to go deeper into his starts.
Still, the Yankees have Chamberlain on a tight leash, and have his total number of innings for 2009 around 160. That total is what's going to end up taking him out of the rotation, and land him back in the bullpen.
With Chien-Ming Wang likely lost for the rest of the season, the Yankees need to fill his spot. As of this moment, Sergio Mitre has been filling in for Wang, but if Chamberlain is taken out of the rotation, the Yankees are going to have to try to find someone to fill his spot as well.
There's nothing wrong with organizations trying to protect their young pitchers from injury, but does the constant switch from starter to reliever and vice versa help or hurt them?
Some players aren't able to make the transition from starter to reliever or the other way around. A lot of the time, these young pitchers aren't taken out of a role because the organization feels that they would be better suited doing something else, but because of keeping the innings total down.
Chamberlain was great as a reliever, and one of the best set-up men Mariano Rivera has had in years, but he has also had success as a starter. While it's clear that he can succeed in both roles, all this back and forth seems unnecessary.
Being cautious is one thing, but perhaps being too careful is also a detriment to the team. If the Yankees put Joba in the bullpen for the sake of his innings total, they are going to be down another starter, which would put them in a worse position.
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