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Packages which contain binfmt.d configuration settings must place them in /lib/binfmt.d/. Files in /etc/binfmt.d/ are reserved for the local administrator, and will override any files with the same name in /lib/binfmt.d/. These packages must also include scriptlets to try to restart the systemd-binfmt.service on install or removal:

Requires(post):  systemd
Requires(postun): systemd

...

%post
/bin/systemctl try-restart systemd-binfmt.service

%postun
if [ $1 -eq 0 ]; then
/bin/systemctl try-restart systemd-binfmt.service
fi