Hi Cory,
I haven't tried them recently to be honest, but knowing some of the ins and outs of the system in terms of Schengen travel alerts etc, whilst you're notifying travel to PPU, your passport will always flag at e-gates. If your PPU told you that it wouldn't it's either because they were lying and didn't like you asking the question, or they didn't know the answer but also didn't want to look like they didn't know so just gave an answer, if that makes sense.
The real test will be when you come off notifying. What SHOULD happen is that the alerts will no longer be there and you'll be able to use the e-gates again like anyone else, but this hasn't been tested yet so we wait to see.
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