If the document has been saved as a PDF and then converted back to word you will have lost all of the formatting before being saved as a PDF.

Any formatting you are currently seeing is words interpretation of the saved pdf.

You are probably best redoing all the formatting in the document.

Sorry to be the bearer of bad news.

If you have a saved version of your thesis in Word format it may be possible to help retrieve the situation but it's likely you'd need to send the document to a volunteer for examination.