Hello. The way ACI is constructed is around an object model. This is to say you create the model you want in APIC (i.e. make configurations). To be smart with physical resources, APIC will only program these configurations (what we sometimes call the "logical model") only down to the hardware where it is needed, when it is needed. In the UI, you sometimes see options labeled "on-demand" or "immediate". On-demand is the default, and it works as I described above. Immediate means you tell APIC to program this config on every leaf, without caring if anything there actually needs it.
This is why you can decommission your remote leaf and still see configurations in APIC. At that point, they are just logical configs that are not programmed in any leaf hardware at the moment, but APIC never assumes you won't want to use them somewhere else. It is up to you, as the fabric admin, to decide when to delete configuration.
So where do you start? Well, one idea is to use the "operational" tab under things like EPGs. This will give you a summary view of all endpoints that are a part of the EPG, their MAC/IP, and where they are connected. If there are on EPs in the EPG Operations Tab, you can safely choose to delete it. Here is a view of that tab from my lab.
Then you can move up to the bridge-domain level and check for any associated EPGs before you might decide to delete. There is a free (and very well done) app on dcappcenter.cisco.com called Policy Viewer which makes a clear drawing of all the objects and what they are connected to. I use that all the time to help decide on things like configuration and even troubleshooting. It even shows you what hardware got programmed, so you can validate that any config you decide to delete was only running on the remote leaf (or not running anywhere at all).
Here are some screenshots of the Policy Viewer.
And focusing on a given EPG and drilling down to where it is programmed
