Since you are using same domain scope for new version of shibboleth, it will be enough to change the idp keys to new keys in Federation registry. (Note : When installing shibboleth, running IDP server(Which is already registered in fr.ac.lk) will have to be shutdown.)
Every institute has a administrator for the IDP,(If the Administrator is not there for the assistance, please contact LEARN TAC and do the needful to get the user account in fr.ac.lk for institutional IDP)
How to change the keys
Log in to fr.ac.lk with the login credentials you received when you enabled the IDP in LIAF.
Step 1: Click on Identity Provider on the main tabs and Search for your Identity Provider in the list
Step 2: On the tabs, there is a "pencil" on the left corner click on that, then select edit IDP.
Now you will be able to edit the fields.
Step 3: Slect "Metadata" on the tabs and select "Certificates"
Step 4: Delete the certificates and paste the new certificates(either Open your entity ID on a browser and copy or navigate for idp metadata file and copy the the keys and paste)
Step 5: Click on "update"
Step 6: Test on sp-test