I'm surprised that it's trying to run migration. You should have an lldap_metadata column with the version number which should be 8+ (don't remember the exact value)
I wouldn't want to have to translate the migrations into a different format, that seems risky. Why is running the migrations as part of LLDAP startup a problem?
It sounds like you can have a simple flyway migration that just creates an empty DB, and let LLDAP populate it on first run (you don't need to create the schema in advance)
Or if you want pre-existing data in the DB, then it should already be pre-migrated and it's just a matter of copying it to the new DB, which is not a migration?