Which modules are updated during a module update?

[Tomi14]

All modules are in the /modules folder, but they are also in /themes/themename/modules

When I want to change something, I change once in /modules and once in /themes...

However, I wonder if when updating, both are updated? I've made hundreds of changes to files, and no update has ever lost my work.
I wonder if the module files used by the store are up to date?
Is the update happening on /modules, and the store uses old files in /themes/...?

[endriu107]

All files in themes/modules/module_name are used to override same file in modules/module_name so when you update module in BO it only have affect on file in  modules/module_name.