preacher wrote:
So how does one "chop" a whistle and how does that affect intonation
If done right, what it does intonation-wise is bring the whistle up a semitone.
On that link people give specific measurements, I'm skeptical about that because I have multiple Generation whistles of the same key that have different tubing lengths. So the specs that work for one Generation Bb might be wrong for another Generation Bb.
Here's the photo I've posted before that includes my chromatic Generations (my new C# is actually a Walton).

Here's all of those played.
https://www.youtube.com/watch?v=7-fQhvleWq8Being that Generations vary, my approach is trial-and-error.
To make a Generation Bb into a B, or a C into a C#, or an Eb into an E, do the following in this order (there's a logic to the order of operations)
1) chop the top of the tube until these notes
xoo ooo
xxo ooo
xxx ooo
are in tune to the new target pitch. (What would be B, A, and G on a D whistle.)
2) chop the bottom of the tube until this note is in tune to the new target pitch
xxx xxx
(What would be Bottom D on a D whistle.)
3) you will now find that this note
xxx xxo
is flat. Carve out that open hole, Hole 6, until the note emitting from it is in tune. (What would be E on a D whistle.)
4) you will also find that this note
xxx xoo
is flat. Carve out Hole 5 to bring it up to pitch. (What would be F# on a D whistle.)
In the photo above you can see the carved-out oval Hole 5 and Hole 6 on the B and C#.
Notice I've not mentioned
ooo ooo
or
oxx ooo
This is because I have found that the note that would be the crossfingered C natural on a D whistle is fine.
If you want open C#
ooo ooo
in tune at the whistle's baseline pressure you'll have to carve the heck out of Hole 1 on most whistles, modified or unmodified, which usually spoils the crossfingered C natural.
Personally I want crossfingered C natural to be in tune, which usually means that open C# is a hair flat. That's how all my whistle are.