If you had an update on kernel tools (which I'm betting you did)
It has to go through *ALL* of the initrd images and regenerate all of them. Its just going to take a long while, period. As long as its working, let it. Kernels aren't anything to screw around with.
Next job for you when this is done...
do these commands:
To find out what kernel you are currently using:
uname -a
To see what all you have installed, as kernels on old systems are typically NOT removed on Debian based systems, rather they are installed not upgraded. Which means you have probably every Kernel installed since the beginning of time on this machine.
I recently had about 50 kernels installed, but cleaned them all up and removed all but the new "known good" kernel I trust and the newer ones since then. Now I am down to 11 kernels.
Still takes forever on re-doing the initrd images though. They are being anal retentive about making sure everything is in there as they have moved to UUID disk naming convention and this has created some anomalies if things aren;t all there.