What are the best practices for entirely removing a custom module?

We have a number of custom modules that were added over the past 14 years, some were added back in v6 before sidecar, before QLIs, before we knew better... 

All modules started their life in Module Builder in our developer environment and were added via Module Loader, then subsequently changed in one way or anothoer with adding relationships, custom formulas, custom Expressions and more...

Sadly some are now redundant, or retired for whatever reason, the data will be archived, but the modules can just simply be deleted in their entirety: relationships, formulas, dropdowns that are used only in that module, subpanels... the lot.

Because of their history they are not necessarily "Uninstall"-able from Module Loader.

So what's the right way to delete them?

FrancescaS