Here's what I did:

I opened a big instrument, in my case, Black Grand Ambient. I then saved an articulation file for this instrument.
Then I exported all folders containing the samples.
I then opened a new instrument and imported the folders to this instrument and opened the articulation file.
It says that "The instrument you are importing were saved from a file whose wave pool doesnt exactly match the current wave pool" and then the mapping of the samples get's all messed up, Everything looks ok, but there are wrong samples on wrong note and on wrong velocity layers.

Now, how can this be? I'm planning to make crossgrades for the Black Grand, but this kinds of slows things down.....

Any idaes?