Hi Ben ,
a little of your question was cut off but I think I got the gist of it.
I would not use save as part for assemblies that are going to change, this is generally a function used of assemblies from outside sources as after you save as a part you are dealing with bodies.
I understand you were doing this to save some of your assembly performance but there are many other more efficient tools for this, I assume since you are utilizing preserve reference geometry you are using SOLIDWORKS 2017 so have you tried Speedpaking instead?
in SOLIDWORKS 2017 we can save planes, sketches and curves inside of Speedpaks so they are very easy to use and will probably yield the most dramatic performance increase to your assembly.
also make sure all your part qualities are set to a reasonably low setting to reduce graphics triangles and use the Assembly Visualization tool under the Evaluate tab on the command manager to troubleshoot slow to open and slow to rebuild parts and assembles.
Scott, thank you for your input.
I am aware of the speedpak functionality, and I used the packaging for the large assembly only for example (though that would be one reason where I might use it anyhow). I still have other cases where I lose references after replacing components.
Anyhow, I am still interested in the main question: is there any way to preserve sketch relations after replacing the part?