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Do you know also the offset of the background on the player side (the half circle on the left with your Pokemon)?
I changed succesfully the first, but for a better result i need to change both =D
That pallet isn't able to be accessed via APE and needs to be edited by hand in a Hex editor. Colours 1, 2 and 10 - 16 are loaded from the pallet you just edited while the seven remaining colours are the ones you need to change, making it unintelligible to APE. You should be able to see this in the third and fourth rows of the VBA's pallet viewer on the left hand side. Anyway, these seven colours can be found at 0x24824. Be careful of the rogue '01' in between the two bytes of the fourth colour - Just leave it where its/ work around it and everything should be fine.
Just to make it clear, here's an image of the data you need to edit: