You shouldn’t be storing customized stylesheets (or any customizations) within the plugin’s folder structure for the exact reason that your customizations will be overwritten when you update.
From the Users Guide section on Customizing Forms:
Once you have created a custom stylesheet, you will need to store it somewhere. It is not recommended that you store it in the plugin folder structure as this may be overwritten in the event of an upgrade.
Yes, there is a way to store your stylesheet outside the plugin’s folder structure. In fact, there are two. On that same Users Guide page referenced above, review the following:
- Specify custom stylesheet location
- Load the stylesheet using wp_enqueue_scripts
As for the customized translation file, there is not a way to load that from outside the folder structure. You should keep a copy of that locally so that you reload it when you update.