The problem here is that in your output document, the rFonts entries in numbering.xml differ from the input document.
For example,
Using xml Syntax Highlighting
<w:abstractNum w:abstractNumId="2">
<w:lvl w:ilvl="0">
:
<w:rPr>
<w:rFonts w:ascii="Symbol" w:hAnsi="Symbol" w:cs="Symbol" w:hint="default"/>
<w:sz w:val="21"/>
<w:szCs w:val="21"/>
<w:rFonts w:cs="Symbol"/>
</w:rPr>
</w:lvl>
Parsed in 0.001 seconds, using
GeSHi 1.0.8.4
is becoming
Using xml Syntax Highlighting
<w:abstractNum w:abstractNumId="2">
<w:lvl w:ilvl="0">
:
<w:rPr>
<w:rFonts w:cs="Symbol"/>
<w:sz w:val="21"/>
<w:szCs w:val="21"/>
</w:rPr>
</w:lvl>
Parsed in 0.001 seconds, using
GeSHi 1.0.8.4
If you look closely, you'll see that the problem is that the input docx contains 2 rFonts elements within w:rPr, when there should only be 1. When the second element is encountered, it overwrites the first. It took me a while to notice that
So you should ensure your input docx does not contains such duplicates. The Open XML SDK Productivity Tools' Validate feature seems to pick up these issues; you also have duplicate Bold elements in your main document part.
It would be interesting to know what app last saved this docx. Was that LibreOffice 6.0.7.3 (per its app.xml), or something else?