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This is indeed a Pandoc problem. From current python:3.13-slim:
root@ae04672dfe5e:/# pandoc -v | head -n 1
pandoc 2.17.1.1
root@ae04672dfe5e:/# cat input.rst
This is some text
.. note::
This is a note
And some more text
root@ae04672dfe5e:/# pandoc --from rst --to jira input.rst
This is some text
Note
This is a note
And some more text
We could potentially find the start of the note by looking for the string \nNote\n\n, but Pandoc loses the indentation, so we can't tell where the note ends.
Now, the Pandoc version in the image we're using is pretty old because the image is based on Debian. Maybe we should use pandoc/core to keep up with Pandoc instead of keeping up with Python.
Anyway, the output is the same with the latest version of Pandoc:
$ docker run --rm --volume "$(pwd):/data" --user $(id -u):$(id -g) pandoc/core input.rst --from rst --to jira
This is some text
Note
This is a note
And some more text
$ docker run --rm pandoc/core -v | head -n 1
pandoc 3.6.2
RST input:
Rendered locally with restview:

But on Confluence:

I wonder if it's a Pandoc/pypandoc problem. It would be best to fix the problem there, as opposed to adding another corner case in this script.
BTW it also doesn't render well on GitHub but that's a GitHub problem and it's documented in github/markup#1682
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