You can use the current audit and job and place a copy of the new file in the bl or remediation package and set to auto-remediate when your audit is job is run. The bl package has a "modify" action that you can use if it deployed to the same path.
just curious ... What is the audit job using to determine the version?
if you have an audit job why not do the 'sync to master' ?
You can also create a compliance job with remediation.