How to not save each part in assembly, when just saving the overall?

I deal with assemblies with many components and subcomponents. Everytime I save an assembly it wants to save each individual part and sub assembly. I have tried going into the system options under external references and set to not save read only parts. This should work with what I'm working on considering we also use PDM and most of the parts aren't checked out. Is there some way to limit the save of each part. This can be extremely frustrating when you have over a thousand parts and sub assemblies in one assembly.

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