Could you give more details about your environment, what you audit and what your
remediation package contains?
I guess that the directory you're auditing contain the conf file defining the SQL connection. When you synchronize, you should replace this file with a one that is not accurate.
Thanks for replying.
All of the contents of the server objects which have been defined as part
of the audit job are common across all servers.
Regarding your issue, it seems that some, or at least one shouldn't be common. If that was not the case, regarding the fact that it what I saw in your audit parts the sync job just push some files, you should not have issue. Excepted if some ACLs or ownership are not well setup in the generated package, depend of options you selected.
Hope this help,