Just an estimate but I would think anything less than several hours would do no harm at all. After your tank has been up and running for months there will be good bacteria clinging to almost all the surfaces. This will be the walls, plants décor as well as in the filter media. At first, I tend to treat things a bit more gentle until I'm sure things are going well but when everything gets settled, the amount of bacteria killed in leaving the filter off is not a large percentage of what is in the tank.
I don't want to mistreat them as they do my work for me but during cleaning there is not enough lost to worry me.
If you do several things at once like clean all the media, clean the walls and move the bottom around so that much of the bacteria may be lost, you might create a problem but just the routine cleaning and shutdown of the filter is not enough to notice.