In a perfect world, you should of course be able to determine, individually for each sector, which of the various applicable frequent flyer programmes you are signed up to should be the one to receive the miles/credits for that upcoming sector.

Unfortunately, we don't live in a perfect world.

Delta - perhaps not completely unreasonably - would be of the opinion that it is meaningless to have both a Flying Blue account and a Skymiles account. (In fact, back in the old KLM/Northwest Days, it was not allowed for US residents to have a Flying Blue account, and it was not allowed for Dutch residents to have a World Perks account; if you moved from one place to the other, you would have to have your account switched from one to the other, also. And yes, I know that Delta is "greater" than Northwest, and that there are no such geographical restrictions anymore - but there's at least perhaps some institutional memory here, and the systems are not quite as user-friendly as you would like, enabling you to pick and choose your chosen FFP at the granularity of each sector).

My advice to you would be - if it makes sense for you to run both a Flying Blue account and a Skymiles account - and for the majority of flyers it would make no sense to do so - to book in a way such that you are not reliant on "changing" the frequent flyer programme mid-trip. Try, instead, to allocate specific tickets to one or the other, and NOT to wish to allocate specific sectors on a ticket to one or the other programme.

Another point perhaps worth mentioning - the FQTV field can hold more than a single frequent flyer number simultaneously. If you find a good, competent agent, who is able to delete the existing entry/entries in the FQTV field, before inputting the "new" entry in that field, you may actually be able to "pick and choose" in the desired manner ahead of each sector. However, by simply "adding" a number to the field, they are actually just adding a second (or third, or fourth...) entry into this field.

When there are multiple "valid" frequent flyer programme details associated with a flight, then you have no way of knowing how the system will respond. The boarding pass will only show one, but this cannot be taken as indication that this is the FFP to which the miles/credits will be directed (as you've seen). Instead, when the system operates to credit the miles: will it prioritise the first valid FFP number entered? Or will it prioritise the last valid FFP number entered? Or will it prioritise the FFP of the operating airline, if such an FFP number is present? You have no way of knowing.

The only fool-proof way, therefore, is to adapt your behaviour such that you don't seek to change the FFP number on any ticket, and so there is only ever a single FFP number associated with any particular ticket. When there is only one single FFP number associated with a ticket, then there can only be one place where the miles/credits will post. So, instead of relying on strategies where you need to "change" the number mid-trip, instead try to book and plan your tickets separately: book and plan Ticket A which will forever and only be associated with your Skymiles account, and book and plan Ticket B which will forever and only be associated with your Flying Blue account.