i would first investigate what cause the problem, if it's only missing php/html file then i'll just copy it from the old cpanel server, so does with the database, just dump from cpanel server and restore it to the virtualmin.
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There is currently no problem, but I'll be doing a lot of imports soon and it's possible something I'll need to re-import something. *If* I needed to re-import, would there be any problems that could arise? It's nice to know how Virtualmin works and oddities of how it works outside of daily operations.