Just a further point of reference...

I used the Garuda website to add my AZ number to an existing (cash, not Flying Blue award) booking. However, that is exactly what it did - it "added", not replaced, the number. The GA website would show both FFP numbers, while KLM still resolutely only showed the existing KL number.

AT check in just now, after a bit of playing around, I managed to get the AZ number to be overwritten during the KLM check in process - but by expanding the AZ number to 8 digits, rather than 10 as I have seen mentioned everywhere.

This resulted in a boarding pass showing the correct AZ number - though there is no direct indication of status, other than the "Sky Priority" red box in the top corner. I was surprised when I actually got as far as generating the boarding pass and seeing the Sky Priority logo, because stepping through the check-in process, it still considered that I had no free luggage allowance and warned me that I could only bring handluggage unless I now paid for a bag with a 50% discount.

Incidentally, looking at the reservation on the GA website, it now has 3 FFP numbers associated with it - the 8-digit AZ number having just been appended as a result of the KL checkin, together with the original FB number, and the 10-digita AZ number added via the GA website earlier...