How to properly update a previously customized marketplace module?

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I've heard it said that when editing a marketplace module, it's best to change the name of the module (for example, prefix it with 'custom') so that when the module is updated, you don't have to worry about overwriting any edits made.  This is something I've done previously.  Keep in mind, my changes include editing one entity in the domain model and 4 microflow.   My question is this: once you have the updated module (SomeModulev2) alongside the custom one (CustomSomeModulev1) made from the previous version, how do you synthesize the two?  There are updates from SomeModulev2 I'd like to import over into CustomSomeModule.  How is this most easily accomplished?  Can I delete CustomSomeModule and keep only those entities and microflows that I changed?  Then can I duplicate SomeModulev2 and add those changed microflows back into the duplicated module?  I'm worried about losing user data if I go this route.
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I always put all customization content in another module. So, let’s say we have module ‘Module’ from the Marketplace, I add my customizations to a separate module, ‘ModuleCustom’. In that way you can always just upgrade ‘Module’ from the Marketplace without your challenges. Since you have added an attribute in the domain model of ‘Module’; I would suggest to move that also to ‘ModuleCustom’. This can be achieved with a new entity in ‘ModuleCustom’ with a 1-1 association to the original entity in ‘Module’. Slightly less elegant, but in terms of maintainability way way better. Is this an option for your scenario? This will for sure not make your tables emptied.

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