Templates behave the same way like standard vBulletin Templates:
Customizations will not be affected by Updates; If customized Templates are no longer compatible they will be reverted.
Also, if you have customized Templates and these Templates no longer exist in the MASTER style of upcoming vBulletin Versions, they will show up as custom.
I don't think that this is a big issue - it just wastes some table space.
The timestamp does not matter - whenever you import a product XML all master style templates with the productid will be deleted first.
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