Because I got some strange warnings from the provision script, I tried to delete the sam.ldb file from the /usr/local/samba/private path and thought, that the provisioning recreates it. It does, but curiously only after the second run.
The first time it breaks with a nonsense message:
Setting up secrets.ldb
Setting up the registry
Setting up sam.ldb partitions
Setting up sam.ldb attributes
ldb load failed: Entry @ATTRIBUTES already exists
smbscript: ejsEvalScript(): Assertion failure
[ 0] setup_add_ldif:12 -> assert(add_res.error == 0)
[ 1] provision:63 -> setup_add_ldif("provision_init.ldif", info, samdb, false)
[ 2] :167 -> provision(subobj, message, blank, paths, system_session, creds, ldapbackend)
It would recreate the whole lot if you deleted the whole lot. While the message is odd (due to interaction with the partitions module) if you delete part of the database, you can expect odd results...