Not sure how to proceed. My end result is I have an Aperture library converted to Photos (new on Mac) and again converted to Lightroom. Trying to decide if I have 3 copies of each picture or maybe one master being addressed by each app. I want to keep about half the total pictures in Photos and the other half in Lightroom. Can't decide how to delete those I don't need in each library (catalog). concerned that deleting in one actually removes it from others.
Depends. You should use "show in finder" Lightroom. In Aperture, see if the image is managed, or referenced. If it is referenced, you likely have both libraries pointing at the same image. Report back and we can provide advice as to what to do next. You do NOT want both libraries operating on the same images. It can be done, but one mistake can make a mess for you.
Also remember that masters and possibly Aperture previews are being copied over. You want masters, and you probably want previews. If you want an archive of your Aperture library, then you will technically have three copies of one photo, but that's how it will be unless you go out of your way to manage them together.