I had the same problem. I just did a make-kpkg with "-revision 2:Custom.2" (my previous custom kernel was "Custom.1") and installed the new custom kernel. I don't know if this is the "right" or "best" way, but apt is cool now.
// joey tsai :: Kenward Vaughan :: > I'm in the middle of a woody upgrade, and discovered that the latest greatest > kernel image has been DL'd and is attemping to overwrite my custom 2.2.17 > kernel. I stopped that process when queried about the modules directory, but > apt refuses to continue with the rest of the upgrade. > > I used aptitude to change the status of that package to hold, but apt-get > still has the script nagging at it. > > Can someone tell me what the best step is to get out of this? Simply let the > image get installed, and reinstall the old (requiring a -f option?)?