I was employed with the federal government for 25 years when I went on LTD for various medical issues. I was recently approved by Health Canada for a medical retirement. Can the insurance company paying my LTD deny paying the top up on my pension?

Your LTD policy contains provisions that deal with pensions and medical retirement. Generally there are offset provisions such that if you get money from another source that would reduce your LTD benefit. You need to examine your specific policy for those provisions.