If I remember right, Batch Monitor affected the compression process in Compressor 2 and below, but ever since Compressor 3, it's a separate and optional application; control (start, stop, hold etc.) of the compression processes were moved into Compressor itself. In fact, whenever I used Compressor 3, I had to launch Batch Monitor manually to see the status. So you should be able to re-open it and keep monitoring.
www.derekmok.com