Assuming that you've got a decent guitar and not something bought from Sears...if it's just the D string tuned up to an E, then no way it's going to hurt the neck. That's no less tension than bending a string during a lead.

On some of the more intense tunings you might want to think about a lighter guage or customizing your string guages but just retuning your D string a little higher isn't going to hurt anything.

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