Hi datformatie,
<blockquote>What is the best method to prevent T3 template / framework upgrades to erase customizations applied to templateDetails.xml, blocks and other layout related changes…</blockquote>
The best method is backuping your customized files for both .php layout & css files. You can use a backup extension to handle this important task or simply create a copy of your modified files.
* Pls try to update our templates/ system plugins via our JA Extension Manager component which allows you to identify which files are changed and which ones will be updated. You can also make comparison and decide which files would be updated, it will be safe for your customization.