You can choose to start the emulated OSGi Runtime with clean storage, i.e. all changes from the Target Image bundle list will be applied as well as the list of application bundles from Bundles tab will be refreshed in the runtime. Go to the Main tab of the OSGi Runtime launch configuration and check the Clear storage box.
If you have changed the bundle list in the Target Image or Bundles tab, to apply the changes successfully, the OSGi Runtime will be started with clean storage and will have only the bundles from these tabs installed.
If you want to start the OSGi Runtime without changes in the list of installed bundles and with faster boot up, the Clear storage box should be unselected.