Custom rollout configuration deleting content from the Livecopy

Hi,

When i try to modify my blueprint (source) which would trigger my rollout config(custom) whose action is set to trigger on modify, i see that all the live copies are modified by msm-service but all of their content is deleted. except the change i made on the blueprint is what visible on them ? any suggestions as to why this behavior ? also, i still have my msm configs under /etc instead of /libs/ and i am on 6.5. Since my other applicaitons are working just fine i would assume this is still ok.