I currently had this issue and here is how I solved it.
Problem: I removed some features in my Eclipse installation. After this I was not able to launch two of my Launch configuration, e.g Alice and Bob could not be started due to Bundle not found. However Carl and Dave could be launched.
To solve this issue.
Open the affected Launch-Configuration: Eclipse Main Menu -> Run -> Run Configurations...
Select the affected Launch Configuration and Select Tab: Arguments. In the VM Arguments text insert: -Dosgi.clean=true
Launching should now be possible again. After a succesful launch you can replace the modified configuration with the original one.