Hi Fabricius,
There is one funny thing i forgot to mention. We are not facing this error for some old implementation projects and only facing the error for impl. projects created after a certain timeline. I am not able to figure out what was changed which is causing the copy of documents being created in impl. projects after they are moved to General tab in template project. Could this be related to change in document context.
But anyways thanks for the help. I will try the above solution and test this thing in Dev systems before we go for production. Will keep you posted. 
Regards
Rajat Singhal