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I would have to say it is highly unlikely that the(correct) reinstall of the engine could have caused such a mis-allignment.
Under the shelf is a rubber padding, and under that is the sheetmetal which is the interior portion of the upper engine compartment. Unless the mechanics did a horribly poor and incorrect re-install, I'd look elsewhere.
As for the decklid hinges. If they did not rub before the mechanical work, they shouldn't rub after the mechanical work commenced. I've owned many, none of them had hinges that rubbed. Best of luck.
Rich
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