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What I found so far is that the issue comes from the makehtml.stripLinkDefinitions sub-parser 1.
For the input of the example it matches C1 | C2 as a title and tries to put it back 2. So it
combines blankLines + title, which is \n and C1 | C2 , which then results in the table
being broken.
Summary
Whenever there is a footnote used above a table it will not
be rendered correctly. As a workaround a comment can be
placed before the actual table.
Example
Workaround
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