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Hi
I'm experiencing this same Time Machine popup after running a "backup on mount" scheduled smart update.
It is very odd because Time Machine is OFF, all the backups from the initial one were done using SmartUpdate.
Every time I reconnect the USB drive I see the Time Machine prompt if I want to use it for Time Machine now or later. I always answer NO.
I'm not entirely sure but the following file is created on the USB drive after I select not to use the drive for TM:
.com.apple.timemachine.donotpresent
I believe that when SuperDuper does the next smart update it is removing this file and that is why I get the prompt next time around. I understand that this file is not present on my Mac's drive, so it makes sense that it gets deleted, but just as Spotlight is preserved I think that SuperDuper should do the same with TimeMachine.
Please let me know if I've got it wrong.
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