You can still credit the miles from your 9W flights to Flying Blue. From their site:

Earning possibilities:

You can earn Miles on all Jet Airways-operated flights with a 9W, AF or KL prefix.

You earn:
First Class: 300% – A, F
Business Class: 150% – C, I, J, P, Z
Economy Class: 100% – M, T, Y
75% - U
50% - L, N, Q
25% - S
http://www.klm.com/travel/nl_en/flyi...e_partners.htm