If you're not working with it every day its easy to forget, I do.
It depends on how you made the cusomizations to the docs module, if you've done it via the ACP -> DOCS MODULE -> TEMPLATES -> MODIFY then all your changes will be preserved. Although if anything has changed in the base system you may need to adjust your templates to account for the changes.
If you've done the changes by uploading a skin over-ride to your /skins/(your-skin)/ directory and prefixing it with the module name, eg: jrDocs_index.tpl then it too will be preserved and used after the module update. Same thing here, if anything changed in the base structure you may need to account for that in your template.
If you've changed anything in the module directory itself /modules/jrDocs/* then this will be lost. Shouldn't be editing here, the correct way to do it would be to create another module then adjust via listeners.
What happens when a module is updated is the old version is saved to an old directory, so for docs:
and a new version is added
So the old code is still on your server, its just not used.
How many versions are stored is dependent on whatever the setting is set to at:
ACP -> MODULES -> CORE -> MARKETPLACE -> GLOBAL CONFIG -> GENERAL SETTINGS -> MARKETPLACE VERSIONS
It defaults to "Keep All Versions" but sometimes is changed to save server space. Check what that is set to before upgrading, make sure its at least 2 in your case so the old version is not immediately deleted.