I always keep my QT running, will even feed the bacteria, or keep a fish in it. The ONLY time I start over is if a quarantine failed and I lost the fish, then I sterilize the system. Remember, when you release fish from quarantine to your DT, they carry anything from the QT with them, so there is no reason to think of your QT as being "contaminated".
The most important reason to maintain the QT operational is that it will be ready on a moments notice and will have a well-established "microbiome". Bacteria in a bottle supplies nitrifying bacteria, but there are whole classes of other fairly important microorganisms that are helpful - chitin digesters, bacteria that decompose fat, etc.
Jay