Actually, the PT/FT games only say that the seeds/fish are FROM Isola. There's no mention of actually still being ON Isola.

Although, that could be in VV3..? What IS on the north side of the island anyway? hehe

There is an island event (I think it's in VV1) where a guy arrives in a boat and is caught taking seeds from the various plants. You have a choice on what to do... but I won't put up the spoiler for that one...

I hope that helps!