Starting Thursday, iPhone app developers will have no choice but to test against iPhone OS 3.0 if they want to guarantee their places in the App Store, and have been warned their existing apps may be pulled if support breaks.

The release of iPhone OS 3.0 beta 5 has been accompanied by an e-mail notice to all registered developers that their code “must be compatible” with 3.0 from here on out if they expect the software to be published. While Apple believes many current apps will run without a hitch, it cautions bluntly that programmers shouldn’t assume apps built for 2.x will carry over smoothly.

“If your app submission is not compatible with iPhone OS 3.0, it will not be approved,” the message reads. “After iPhone OS 3.0 becomes available to customers, any app that is incompatible with iPhone OS 3.0 may be removed from the App Store.”

Apple doesn’t indicate whether submissions will have to be complied using the 3.0 version of the iPhone software developer kit or if it only requires that apps be tested using a 3.0 emulator or device.

This is good for consumers (those who update will have apps that work without worrying about version issues), but could be a roadblock for developers for awhile.