You can certainly highlight text in mobi and ePub files.
I'm not sure how with mobi, but with ePub, the highlights are saved (I believe) to a separate file in the reading system. With the T1, this file can them be exported to a PC using the Sony software. I'm not sure how it would be done on other devices, but once on the PC, you should be able to view the ePub with the highlights shown in the Sony software - might even be able to see them in ADE.
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