dm Server provisions fragments from the repository when deploying hosts which the fragments refer to. See com.springsource.kernel.userregion.internal.quasi. DependencyCalculator.satisfyHosts.
-clean deletes the work directory including the deployer's recovery log which means that deployments are not replayed automatically. Artifacts in pickup are processed but programmatic deployments have to be repeated.
When -clean is not specified, we replay the deployment of the artifacts listed in the deployer's recovery log. Note that we clean start Equinox on every restart because we don't trust the contents of Equinox storage if there has been a crash (we tried this for a period in 1.0 but found that it was subject to corruption).
This should be the behaviour for the plan+fragments scenario you describe. The restart behaviour should simply depend on whether the plan is deployed or not. Dependency calculation will be repeated if the plan is deployed.