Remove the old file (see https://help.researchgate.net/hc/en-us/articles/14293099743121-How-to-make-content-private-or-remove-it for instructions), then upload the new version.

It depends on whether you want to keep the old version (especially if it has been published in an academic journal or presented in an academic conference) or not. If you want to keep it, you may upload the new version marking this accordingly. Otherwise, you may remove the old version and upload the new version in its place.