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You can use Nessus for this. It has a plugin for finding data at rest which could be used for this kind of application. One advantage of using a tool like Nessus is that it already has options set-up for authenticating to various types of system over a network.
This does not come from the scripts you have used (tuxlite). Although it is a bad practice, you can frequently find linux processes using deleted files (Apache in your case). RKhunter doesn't like that too much, as basically those files are invisible to other processes and this could be seen as malicious behaviour. However, in your case and given that this ...
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