Update dnsmasq conf file overwrite original

pihole command line update, pihole -up work well but dnsmasq.d directory conf-file, 01-pihole.conf overwrite original setting.
so, logfile-facility setting define original.
and other log-facility(ex:02-pihole.conf) setting conf file occurs ERROR, not work DNS.

any way to avoid this file over-write?

This is by design, and is noted at the top of the file:

As also noted in the top of the file, anything you want to add should be in a separate config file under /etc/dnsmasq.d/whateverfilenameyouwant.conf

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