I am trying to transform Docx to TEI using oxygen XML editor with Docx TEI P5 transformation scenario. My word document has some footnote and some hyperlinks in footnote. When I transform into TEI then hyperlinks are lost. They are referred to sometime settings.xml, styles.xml, footnote.xml etc. But no mentioned of original link.

This sounds like a bug. Can you supply a test file, please?

Secondly Font size and spacing(center alignment) in the text also lost and all text converted to single font. 

That's harder. The transform was designed to ignore font size and spacing deliberately, as they don't contribute to semantics. 

I can show you next week where you would look to add support for this.

Sebastian Rahtz