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You should be able to paste a blueprint over existing machines to change recipes and add modules.
(do correct me if I am wrong of course)
Sorry for not having a better answer, I tried a few ideas in sandbox but none of them worked.
I would love if they would be applied with a shift-clicked BP placed over the top (as Nailfoot suggested).
There are some mods that can help though (assuming you use mods):
https://mods.factorio.com/mod/CopyPasteModules
https://mods.factorio.com/mod/ModuleInserter
The following mod appears to allow modules to be added with an upgrade planner.
https://mods.factorio.com/mod/upgrade-planner-next
I am not sure if the upgrade planner built into version .17 can do this.
it is possible, but you need to configure the upgrade planner beforehand.
If you place it in your inventory and right click, you can specify filters for which entity you want replaced by which other entity. This can also be done with modules.
This also allows downgrading btw.
Sorry if this comes a bit to late for you, since this was my first google result for this problem I wanted to share the solution.
I now use this great mod:
https://mods.factorio.com/mod/ModuleInserter
However, I will follow your solution the next time I play vanilla.