Do I understand it properly that you had pushed the axle out of the hub to do your work, and now you were drawing it back into the hub by using the axle nut to pull it through?

From what I read, and what I did, is very, very thoroughly clean the axle splines and the internal splines inside the hub - I used a small wire brush and penetrating oil and did this very thoroughly. I had read that if one does not do this, the axle can bind going back in. I did not attempt to draw it in too much with the nut until it was mostly through and seated in the hub. I was able to push and pull on the hub and get the axle to slide almost all the way through. Also, if you pull back and forth on the hub to seat it on the axle, make sure when pulling, you do not pull the inner CV of the axle joint apart.

You might be able to pull and slam the hub down onto the axle several times to get the axle to seat further, but if you were seriously wrenching on it, there is doubt this technique would move the axle through further. It might be pretty bound up. Perhaps spraying lots of penetrating oil into the splines could help if you were trying to seat if further through some type of force or impact.

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2003 X5 Sport w/Premium Package M54 3.0L 6cyl