Grub, post clone, problem (but it still boots and works OK).

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http://www.linuxquestions.org – For backup I alternate two 1TB drives (I plan on adding an additional backup disk some day). Every few weeks I clone my working drive to the other one. I then use the newly written drive as the working drive and keep the other on a shelf. This worked OK until the 2nd of August 2013 when an update to the OS (Mythbuntu 12.04) could not find grub. It expected to find grub on the drive that was the source for the last clone (I assume). Help screens got me through this, so everything works just fine now. My question: How do I avoid a repeat of this ? Post clone is there a file I can edit (or rest (HowTos)