Running samba-tool dbcheck to remove links to deleted objects and (only in master) samba-tool domain tombstones expunge to clean up old deleted objects should not increase the USN.
Fixed in Samba 4.5.1 with c5a0fc082959d4fba5e76831e9b952e947d99eb3 from master commits ending with 0ab32637249fb88917d240e78c0f213b83236027.