I suppose it's Fret dressing time..

[mandroid]

As I get up towards the A, Bb & B on the E string , Mix A5,
the arched fingerboard's frets wear such that they no longer note as a unison pair.
and have become rather dissonant..

Even the Tuner agrees.. the 2 strings are fretting several cents off ..

so I suppose as all the previous topics on flat or arched fingerboards ,
are recalled , the fact that the flat fingerboard
of my 92 year old A4 still notes in relative Unison, where the much newer one

wears unevenly, adds a certain additional factor to the discussion..

[Michael Lewis]

Are you certain the finger pressure is equal on each string of the pair? I suppose it is POSSIBLE that the fret wears differently under one fret than the other, but I think that would be the result of uneven finger pressure as a habit. It's normal to see some wear on the frets, and with a strong magnifying lens you should be able to see if the wear is uneven.

One distinct possibility is uneven strings. You CAN get a bad one, or one may have been stretched over it's recommended tension, which will make it deform along it's axis.

[Tavy]

This can also be caused by uneven nut height for the two strings - or worse - a chip breaking off the front edge of the nut effecting one string only (which will then go very sharp when fretted).

[bmac]

Yes,,, I would be suspicious of the nut more than the fret..

By the way you might be able to get by by replacing the first five frets or so rather than refretting the whole thing. Nut replacement and adjustment is not terribly difficult either, just a bit tedius. See Frets.com.