I think I have at least a few answers to my question:
Most of my problem was actually caused by a custom script I was running. Running the script at the end, rather than the beginning, allowed my changes.txt edits to take place. I'm not sure why, but that seems to be the answer.
Also, I think that "." doesn't capture new lines. Both [.\r\n] and [\s\S] seem to work to capture everything.
For some reason that I really don't understand, this worked:
'\\v \d+ LATER([\s\S]*?)(?=\\v)' > ''
but this didn't
'\\v \d+ LATER([\s\S]*?)\\v' > '\\v '
[Side rant: I really miss when the forum allowed Markdown.]