Thanks for all the replies. It is indeed a single ticket so I wasn't anticipating all this uncertainty.

Transavia keep saying I should get a boarding pass for the second leg from LBA. KLM are saying they have had a change of policy and can no longer do that and that we need to check in in Amsterdam.

Transavia have escalated my query and now say I "might" be able to use the self service check in kiosks.

I don't understand why there's so much uncertainty. It doesn't seem like a complex travel situation.