Flow should be unaffected.
Seed the new filter media with bacteria that (if your tank is >5 months ish old) will be living in the gravel substrate.
Mulm
Mulm is nitrifying bacteria along with its carbon based food source, decayed plant material, fish waste detritus, invertebrates, diatoms, other algae, BGA etc. It is loaded with organic matter, bacteria and fungi, as well as a source of food for them. It can therefore be considered as active living thing and adds precisely what's missing from an established tank to a new one.
Deep Vacuum a substrate, let the water settle in the bucket, the dirt on the bottom? That's Mulm.
The dirt in the filter sponge is Mulm.
This is the wet "dirt" left on the bottom of a water change bucket after vacuuming the gravel. You wait about 2-5 minutes and pour off the clear water, save the wet soupy stuff left over and add this to your new filter media.
Disgusting I know...