Paratext doesn't directly manipulate the text as it is displayed - this would be done by the combination of the Firefox browser based HTML control we use and the font being used for your project.
We did upgrade the HTML component between Paratext 8 and Paratext 9.4. The control in Paratext 8 was based on Firefox 45 and the control in Paratext 9.4 is based on Firefox 60.
On the Advanced menu of the Project menu, there is an update to export text as HTML. You could then try opening the file in Firefox to see how it displays there - if it displays correctly, it may be a setting that we are using for the control and you can create a problem report in Paratext with the details and the sample HTML.