I faced this issue now a couple of times (using maven/tycho):
Defined plug-ins from the target-definition file change version and go missing in the p2 repository.
This is kind of annoying because a previously building project does not build anymore. How do you solve this problem? Update the version each time this is happening?
If you are building against a p2 repository with changing content, like for example the Integration builds repository of the Eclipse Project, you probably want to use the "0.0.0" meta-version in the target file. Just replace all versions in the target file with 0.0.0 and Eclipse and Tycho will just use the latest version which is available in the p2 repository.
Note however that you should only use mutable p2 repositories during development. For releases, you should only use p2 repositories which are immutable in order to ensure that your project can be re-built in case you need to provide a patch release.