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Clone HDD - Source disk modified

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Using Acronis True Image 2015, Clone disk function.

Source HDD has a special Linux on it. Before I clone it on another HDD I got next warning message:

https://drive.google.com/open?id=0BwXmKaSw75eKLV83VnhITFdiMUE

Does that warning refer only to the destination disk? Or refers also to the source disk?

In other words, when a clone HDD function is performed, does Acronis any changes also on the source disk?

The problem is that my source disk worked prior clone function and does not work anymore after that. The files are there, but is not proper initialized anymore.

The source disk contains a special version of Linux operational system on it and is used in a hybrid satellite receiver Panasonic TU-HMS3.

What can you tell me about that?

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