First let me join Lisa in the sorry, it is very tough to lose a pet.
If I go too fast or do not explain something well enough let me know.
The biggest issue you are facing is that it appears your tank is not cycled or is experiencing a mini cycle.
Either the tank is newly setup (say in the last 3 months) or your maintenance needs some adjustment.
Also what size tank do you have and how many fish are in it.
When you clean the filter do it in a bucket of tank water, tap water may contain chlorine which would kill beneficial Bacteria.
You can also use tap water if you you use water conditioner to remove the chlorine/chloramine first.