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I was wondering how will this affect my pr and indexing by google will I be penalize for doing so. and is there a way to do it so if I wont be penalize if this was to happen.
This is the very essence of the canonical issue - Google, if it has indexed your site without the www in front, will see the changed links as pointing to different pages - this may cause duplicate content issues if it already has that page under another url (ie without the www) in its index (as mentioned in many posts on this website).
does this produce results with www in front or not?
Do other people from other sites link to your pages with or without the www?
Pick the majority and stick with it, setting up 301 redirects from old non-www pages to the new ones at the very least.
Hmm, this sounds like it may be my problem. Could you please tell me how exactly would I check that?