However it seems that this is because I was installing the very same
file (name & content are identical) from my hook scripts.
fix your hook then?
Die hook itself is fine, there is basically nothing to fix.
Let me shortly explain what I am doing: I have a Git repository containing system configuration files. This repository will be initially installed by a hook script (mainly copy/link the config files to their respective destination folders). There is also a file for /etc/apt/sources.list.d which is currently an exact match of the one in /archives.
The reason behind is simply that I am doing an update of the system configuration files via "git pull" (with a bit of magic around) and that I would like to be able to update the APT configuration too.
The question is why I can't have a hook putting a file under /chroot/etc/apt/source.list.d with the very same name as in /archives. IMHO the existing file should simply be overwritten instead of giving an exceptional error...