Technically the notes between E harmonic minor and B Phrygian dominant are the same, but I think the functional context would be different. Correct me if I'm wrong, but I think E harmonic minor would be appropriate for a single chord shift within the context of E minor (which this is), whereas B Phrygian minor would be what you would call the mode in the case of a full-blown modulation where B becomes the root note for a full subsection/subprogression, like in the instance of a secondary dominant sequence.
Of course, this is all getting down to nitpicking terminology. For your purposes guitarreverie, the notes are completely identical, and the distinction between E harmonic minor and B Phrygian dominant isn't really that important.
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