It's a good idea to run a diff on your current version and the new version. For example, if you're running 3.6.1 and e release 4.0.0, run a diff on the official versions to see if any templates changed that you may want to merge.
However, if you clone the client templates you can modify them without risk of them being overwritten.
~/app/views/client/bootstrap is the default client template. Copy and rename the bootstrap directory to something else. Then, select it for use under Settings > Company > Look and Feel > Template
Still, it's important to run a diff to see what's changed, or some things may not work properly.