LINQ or Lambda for two foreach query
First thing I'd suggest is make the 2 lists the same type(string).  Now the file list can be an exclusion list that contains only the filenames that aren't in the database.  Something like this should work:

    var clientDocList = documentRepository
        .Documents
        .Where(c =&gt; c.ClientID == clientID)
        .Select(d =&gt; d.DocFileName
        .Trim()
        .ToUpper()).ToList();

    var fileExclusionList = Directory
        .GetFiles(directoryPath)
        .Select(x =&gt; Path.GetFileName(x)
        .Trim()
        .ToUpper())
        .Except(clientDocList).ToArray();