I could resolve this issue by myself.
According to the lxd database documentation, it seems that I could delete unnecessary settings at startup by putting a patch.global.sql under /var/snap/lxd/common/lxd/database
with query to delete old setting records.
So I confirmed the unnecessary records by
$ sqlite3 /var/snap/lxd/common/lxd/database/global/db.bin
sqlite> select * from storage_pools;
...
sqlite> select * from storage_pools_config;
...
and created a query to delete those records.