It will deplete the bacteria population considerably. I assume the tank is fully cycled now so it isn't really as bad as it sounds. A new filter on an already cycled tank will get a good bacteria population fairly quickly. Especially if you seed the new filter with media from the old one. If it will only take a few hours to take the old filter back & then get the new one hooked up, just pull a bit of used media out of the old one & put it in a bucket with some of the aquarium water. If it is going to take a full day or more, spend a couple of dollars on a air driven box filter & just stuff the media in that, leaving it running in the tank. When you get the new filter home simply take the media from the box filter & stick it in the new filter.An extra
water change or two for the first couple of weeks will help keep toxin levels under control to. Get
ammonia,
nitrite &
nitrate test kits if you are really worried about it. Then you will know if things are getting bad for the fish & know when the filter is cycled fully again.
Be sure that it is a cracked housing or retainer before you take it back to the shop though. That is a fairly rare problem & I have only experienced it once myself & haven't heard of anyone else having that problem. More likely the impellor is just worn. How old is the filter & how often do you clean the impellor housing out?