Simon, the best way is to remove the rail, clean all the old mastic off both rail and van, apply new mastic and replace the rail.
Removal is by taking out the plastic fill strip along the length of the rail, under this are lots of screws, many of which wil probably be rusty.
Remove them all, and use new stainless steel screws when replacing the rail.
Ease the rail off the van taking care not to bend it.
scarpe the majority of old mastic off th erail and thoroughly clean with white spirit.
Use a plastic scraper on the van to remove most of the mastic , clean all the remainder off with white spirit.
Apply new mastic, either ribbon type or Silkaflex gun applied , and replace the rail.
Refit the fill strip.