Thanks for the question and your suggestion. Rest assured, custom templates and all of your option settings persist unchanged whenever you update to a new MLA version.
You can also back a backup of your templates and settings from the Settings/Media Library Assistant General tab. Scroll to the bottom of the page and click “Export ALL Settings” to create a backup file. You can create as many files as you like; they are date and time stamped so you can restore the one you want later.
In addition, you can deactivate and even delete the plugin without losing the settings. They will be there when you reinstall and activate in the future.
You can permanently delete the settings and (optionally) the backup files if you are removing MLA for good. The “Uninstall (Delete)” Plugin Settings section of the General tab enables these options.
I am marking this topic resolved, but please update it if you have any questions about preserving your templates and settings. I will add this explanation to the FAQs.