Thank you for your inquiry.
If your bubbletrap is a sponge, then yes I would recommend cleaning it otherwise it can start to cause issues with nitrates and/or phosphates from the detritus trapped within it.
What I would recommend doing to help "save" the copepods that live in it is to rinse the sponge out in a bucket of tank water. That will allow you to save the copepods in the water, then strain the water through a net when dumping it down the drain. You can then put the pods back into the fuge that got caught in the net.
Pods will be able to pass through pumps without any issue, some may get chewed up, but a majority will go through without any problem.
If there is anything else we can do for you please let us know.
Marine Depot Customer Service