[calorie]

Yes, there are some mods that change templates without you having to do it manually. There are also other mods that add their own templates. Mods that change templates on the fly usually do a search and replace, so if you manually change something in a template, it is theoretically possible that the on the fly change won't occur. There are many mods that require edits to the default vB templates. The best thing to do is keep a running file of what changes you make so you can undo or redo them when necessary. If you ever need to get back to a default vB template, you can simply revert it.