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No, all stuff in the module directory is not meant to replaced dynamic. The only option is to undeploy all applications which depends on, replace the modules and deploy tha app's again.
In this case the module is unloaded. The other possibility is what you describe.
Beside from the technical difficulty, if you share a module it will not good to replace it (dynamic or static) without knowledge what the effect to all applications is.
So the most common way from my experience is to create a new version to be sure that existing app's are not effected. But that are my two cents.
Thank you for the info.