Moving account with add on domains

I'm in the process of moving my addon domains from a 3rd party host to my own dedciated server.
Most of which I've done.

I have 3 domains left.

The home domain - example.com
with 2 addon domains underneath this.

(Note addon domains and not sub domains.)

If I change the nameservers for the home domain, will this affect the two remaining addon domains.
These two addons will still have thier own entries at registrar level.

The two addon domains in question, I'm hosting for a friend who won't get around to migrating his data for a few days.