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If the file server is a windows machine you can disable the last modified update in the registry. This will increase the performance in a large directory quite a bit while it converts each file.
I'd also recommend you run Profiler or similar on the 'selects' the MP3 server sends. Create an index specific to that select and be sure to add the result set as the included columns. That will make the DB query to identify the files very efficient. Unfortunately you will see that the company ID’s that are higher will be lower on the order returned.
Other than that, you will be depending on CPU and base file system IO to work the backlog.