Whether you agree with Apple’s not-so-subtle message to Palm and its Pre users or not, the battle lines have been drawn. I don’t, however, believe this is a slam dunk win for Apple–Palm is going to fight back hard. On Tuesday Apple issued a support note warning customers who sync their third-party devices with iTunes that it might not work in the future. Apple never specifically mentioned Palm, but the warning comes just days after it was released and a few weeks after Palm demoed the Pre syncing with iTunes.

Apple’s support note reads:

“Apple is aware that some third-parties claim that their digital media players are able to sync with Apple software. However, Apple does not provide support for, or test for compatibility with, non-Apple digital media players and, because software changes over time, newer versions of Apple’s iTunes software may no longer provide syncing functionality with non-Apple digital media players.”

To be clear, Apple has every right to change iTunes, effectively breaking the ability for third-party devices to sync with its applications. In the digital media market, iTunes is the center of the universe for Apple and its devices.

However, Palm is not going away that fast. Today’s Palm is not the same company we all watched in the late 90s and 2000s like spectators glued to on oncoming train wreck. Palm is different now.

With Jon Rubinstein at the helm, Palm feels like a scrappy upstart company that is more than willing to take on the Apple fight. Until recently, Palm was a train wreck of a company, but I don’t think they are anymore.

Rubinstein, who helped conceive the iPod and was part of Apple’s executive team for many years, knows the Apple game better than anyone. He knows how to play it and win–after all, he was on the other side of the fence for a long time fighting the game for Apple.

That’s obviously how Palm managed to get the Pre to sync with iTunes out of the box. Rubinstein is not the only former Apple employee currently working at Palm–there are more there than you may think.

I was glad to see Palm stand up and respond to Apple’s note with a statement the company sent to me yesterday.

Palms view of the situation is this:

“Palm’s media sync works with the current version of iTunes. If Apple chooses to disable media sync in a future version of iTunes, it will be a direct blow to their users who will be deprived of a seamless synchronization experience. However, people will have options. They can stay with the iTunes version that works to sync their music on their Pre, they can transfer the music via USB, and there are other third-party applications we could consider.”

That speaks volumes. If Apple does disable the syncing feature, we have other ways to make it work.

This is going to be an interesting battle and is sure to heat up over the next few months. Don’t expect Palm to fold quickly though.