Using "id" causes problems in some cases, because of overlap with the id part of pandoc attributes. Note that the Docx writer will still interpret an "id" attribute for legacy compatibility, so if you use markdown files that specify "id", they should still work.
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% pandoc -f markdown -t docx -o - | pandoc -f docx -t markdown --track-changes=all
I want [I left a comment.]{.comment-start id="0"
author="Jesse Rosenthal" date="2016-05-09T16:13:00Z"}some text to have a
comment []{.comment-end id="0"}on it.
^D
I want [I left a comment.]{.comment-start comment-id="0"
author="Jesse Rosenthal" date="2016-05-09T16:13:00Z"}some text to have a
comment []{.comment-end comment-id="0"}on it.