So, if any change was made to the master installation, equinox was dropping user installed bundles (in majority of cases), but P2 was totally unaware of that change.
In other words - if you installed any feature, it was lost, and you could not reinstall it, because P2 still thought it was installed.
I can't say I was totally unaware of changes happening in P2 regarding those problems, but when I prepared a package of latest Kepler release, I got a dialog:
|P2 new feature|
P2 stored a timestamps of important config files during first Kepler launch.
yum changed the installation and touched files
P2 discovered the change and dropped all plugins installed by a user into user space
P2 located previously installed bundles and offered reinstalling them.
I'm sure all devops will appreciate that feature!