[Jawelin]

Templates, as they're upgraded via upgradeXX.php which reads vbulletin.style, are much more complex to analyze 'off-line'.
Great help could give the TBS hack from FireFly, which stores templates as html files you can download before and after the upgrade.
This way, just like the php code, you can manage the differences and restore all the hacked upgrades you loose.
Anyway, all the custom templates aren't overwritten by the upgrade script. Let's say, all those templates you have modified by their interface (those who have the '[revert to original]' button) aren't overwritten.
Only those created new by hack installation scripts and never modified will be deleted.

The problem this way still remains is you'll lack each new template upgrading what you modified. They should be managed by the above TBS+compare procedure.

Bye