Actually, if I recall properly, I think the Lee pin on the 6.5CM full length sizing die is somewhat undersized on purpose so it probably didn't actually push out brass when it went through the flash hole. Should be ok to use but I would go through the lot of it with a good primer pocket cleaner and visual inspection to ensure it didn't push out a burr around the flash hole.
Edit - > I just checked and this may not be the case. I know I had 'turned down' the decapping pin on the Lee collet neck die as it wouldn't fit. I chucked it up in my drill press with a piece of 400 grit sandpaper. The decapping pin on my Lee 'universal' decapper, which I didn't sand down, is still for the larger flash holes and won't fit into the Lapua brass flash hole. I don't have a Lee full length sizing die so I can't check but I suspect it will be the same - too big. Could be you have to check out each piece of brass and make sure the flash hole is flush without a burr after all, and if you have any more brass, turn down the Lee decapping pins with sandpaper. If you don't have a press you can use a drill too.