systemd version the issue has been seen with

systemd 245

Used distribution

arch

Expected behaviour you didn't see

N/A

Unexpected behaviour you saw

my nspawn file was removed from /etc/systemd/nspawn

Steps to reproduce the problem
Import a machine and associated nspawn file in /etc/systemd/nspawn Remove the machine with machinectl remove and the nspawn file will be removed as well.