Updating the Documentation Module
Using Jamroom
Depends on how you've done the customized templates.
If you've cloned a skin or created a new one, then uploaded files that start with the name of the module:
/skins/xxYourSkin/jrDoc_category_index.tpl
Then they are safe, you'll just have the old version of the template file that you'll then need to check to see if there are any changes you want to bring in to your skin override template.
If you're over-riding by using the Template editor on the TEMPLATES tab of the Docs module in the ACP then those overrides will still be there after the update and you can use the COMPARE button to see what the difference is.