Hi Nick Van Drielen,
It is not compulsory to copy all the module files to your new module, if you want to change some logic in microflows then you can copy the microflow to your new module, it is applicable for both email and encryption modules.
check the below link for a detailed explanation.
https://austinmcnicholas.com/blog/2019/2/24/setup-email-in-a-mendix-app-in-10-minutes-or-less-9ya8n
Hope it helps!
Thanks,
Vignesh Rajan.