Toilet anchor collar and sub flooring replacement

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I remover the carpet from the bathroom floor so I could replace it with a new vinal floor covering. I was going to glue it on top of the older covering. I removed the toilet and found the old vinal comming up, I strrted to remove it. I then found the old sub flooring was in bad condition by the toilet. I tried to remove all the old vinal floor but it is still glued to the floor very well except by the toilet. Can I just replace the bad sub floor section and add a new underlayment, will the difference be noticible.
1/2" particle board sub floor, 2 old vinal floors 1/8" apx. new 1/4" underlayment.Also the collar for the toilet is perty rusted, how do I replace it? It is cast pipe and steel collar.