Load of tosh. Nothing at all to do with APD. All Jet2 seats are economy irrespective of extra legroom or not and therefore the standard APD applies.
They are removing the extra legroom seats for two reasons. More bums on seats on their flights and a seemingly lack of take up for the extra legroom seats. Another reason I'm told is that their 757s are non-standard configuration which means if one goes tech (which they do every now and again) it makes life difficult when they come to swap them round. Standardizing the seating will help them get over such problems.
There are still some legroom seats but the majority are being removed gaining Jet2 about another six rows of seats on a 757 I'm told.
Don't believe everything you read on here (except this post obviously!)