Since E.B. still got an obscure debug message about metadata not being up to date, I added debug lines to the remaining places where this could emerge (currently only available from hg).
Using hg from just now - first line looks like what you want:
dovecot: lmtp(testuser@example.com): Debug: U5ZtLH8IAVXydgNAM/SpMA: sieve: file script: Binary reports different script location (script2.sieve' rather than /usr/local/var/dovecot/sieve/script2.sieve')
dovecot: lmtp(testuser@example.com): Debug: U5ZtLH8IAVXydgNAM/SpMA: sieve: binary up-to-date: script metadata indicates that binary /usr/local/var/dovecot/sieve/script2.svbin is not up-to-date
dovecot: lmtp(testuser@example.com): Debug: U5ZtLH8IAVXydgNAM/SpMA: sieve: Script binary /usr/local/var/dovecot/sieve/script2.svbin is not up-to-date