When you overwrite a feature layer (federated, not hosted) with Pro, does a new item get created?...or does the existing item get retained?
If a new item is created, how are you supposed to keep feature layer sources within a web map?...doesn't this essentially break a data source within the web map?
When overwriting, it does not create a new feature service. The item stays the same in Portal and the web maps that contains the feature services will still continue to work.
However, a word of warning when overwriting feature services. In the data frame properties, I recommend checking the box next to: "Allow assignment of unique numeric IDs for sharing web layers."
This comes in handy when you want to add new layers to the feature service in Pro, and then overwrite the feature service. If you do not have this checked, your item ID's can potentially change and it will mess up the web maps that contains the feature services, and you will have to remove and re-add the feature service within the web map. You can avoid this by checking the box. With that being said, if you have already published a feature service without that box checked, then check it and re-publish, your layer ID's might change and might affect the web map.
This link has more documentation regarding sharing web layers: Introduction to sharing web layers—ArcGIS Pro | ArcGIS Desktop
I did a quick test after publishing this post, and yes, the item id of the published map image layer (map service) and feature layer (feature service) did stay the same.
I am familiar with the allow unique assignment ... and for everything you mention ... would definitely recommend this to anyone publishing services with more than 1 layer.
As an aside to publishing services with Pro ... if we want to generate feature layers for our users to consume within Portal or Pro, is it generally best to publish layers individually or publish a map with several layers? For example, say for our real estate division, would it be best to publish 1 map service with several feature layers (address points, parcels, road centerlines, easements, etc...) or publish individual map service and feature services for each layer?
I have gotten mixed answers on that one. It might depend on how many layers you have in your feature service. If you have a small number of layers, I would say leaving them in one feature service is fine. If you have a large number of layers, it's possible separating them out might be beneficial. You might need to do some testing to see where you get best performance.
If you have any data that doesn't change often at all, I would recommend those layers being cached.