If DMVPN use IPSec, related configuration for strongSwan adding via /etc/swanctl/swanctl.conf and reloading configuration with swanctl -q. So, it is not stored inside the strongSwan configuration file permanently and requires reloading with swanctl -q to make configuration active.
Inside ipsec-settings.py in apply function exists ipsec restart operation.
When ipsec-settings.py running after the DMVPN config (dmvpn-config.pl), it restarts strongSwan and, as a result, remove DMVPN-related connections configuration.
If VyOS configured as spoke, this is not critical, as swanctl -q additionally runs by opennhrp-script, but if it acts as a hub, DMVPN IPSec configuration will never being active.