And of course, 10 minutes after sending the above, I found an interesting twist (as I was checking for other places that might suffer from the bug).

First of all, my advice about restoring the encoding is flawed. You cannot define from no encoding to UTF-16, for example (you get chinese garbage). You have to go to UTF-8. So converting back to the original encoding is a no-go; you have to move to UTF-8

Next, I do a lot of massaging of my input before anything else proceeds, using a simple string that contains all the lines. When I operate on pasted text, that text comes in with no encoding, and comes out of all the massages with UTF-16.

So those regex.replaces aren't messing with the encoding. The last of those is this code:

rg.SearchPattern = "(Their scores \(not necessarily in order\)\:.+) \r([0-9])"
  rg.ReplacementPattern = "\1 \2"

  while rg.search(s) <> nil
    s = rg.Replace(s)
  wend

The patterns that appear to cause the problem are:

fMoved2.searchPattern = "(.*)F([1-9][0-9]*)\[([^\]]*)\]-->W([0-9]+) (.*)"
  fMoved2.ReplacementPattern = "\1\5"

So I tried some variants to try and see if it was a pattern problem:

fMoved2.searchPattern = "([^F]*)F([1-9][0-9]*)\[([^\]]*)\]-->W ([0-9]+)(.*)" fMoved2.searchPattern = "([^F]*)F([1-9][0-9]*)\[([^\]]*)\]-->W ([0-9]+)(.*)$" fMoved2.searchPattern = "([^F]+)F([1-9][0-9]*)\[([^\]]*)\]-->W ([0-9]+)(.+)$"

Nope.

This is too weird for a Saturday afternoon.
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