Did you try to upgrade any other catalog apart from the one that is giving you the error?
Also if the above does not work, launch Lightroom 6, and then click on File>Open Catalog and select the catalog of Lightroom 3.6
Have you updated LR6.0 to the latest version 6.6? If not, go to the help menu in LR6 and check for updates. Then try the catalog conversion again.
Otherwise you may need to export the entire LR3 catalog and then import it into an empty LR6 catalog. But it could take time to re-build all the previews, depending on catalog size. You would probably also need to re-create Publish services if any although regular collections will import.
Thanks for the tips. I upgraded to LR 6.6 then I launched LR clicked on File>Open recent and selected my old catalog. It worked! So probably both tips helped for this problem.
Much appreciated to both responses :-)