Most of the bacteria live in the filter media, of course there is bacteria living in the substrate etc. but the largest amount are in the filter.
If there are 2 filters on a tank (I have 2) I would always advise changing 1 cartridge at a time and wait a couple/few weeks before changeing the other, so there is always bacteria working. If they are both changed at the same time, it removes nearly all the bacteria from the tank and may cause a mini cycle, and puts a strain on the bio load again.
I would recommend leaving the HOB filters on the tank for 3 wks or so and also put the new filter in the tank to allow bacteria to start growing in it but not turning it on until you take the others off. You could turn it on as well if the current isn't going to be too strong for the fish-do the HOB'S have a flow control? you could turn them down if turning on the new filter as well.
If you have just put in new cartridges say just yesterday/today then it may not make much difference if you take out the old filters and put in the new one. But there may still be a lot of bacteria in the actual filter chambers themselves which would help speed up the growth of new bacteria. I would also use some stress zyme/cycle or somethng similar which adds live bacteria to the tank and speeds up the process.