That all depends on how you do your upgrades. If you carefully and intentionally compare all files and manually merge changes from the new version into your files (or vice versa), then you'll be fine. But if you just blindly copy all the new files and replace your own without doing any inspections to preserve your customizations, then you will be wiping out your own changes. So, you can see it's all up to how you do it. When upgrading (especially templates) you should always manually merge customizations, not blindly replace things.
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