This sounds like the application of the style sheet has been lost when the project was upgraded. I bet if you right click on a topic and select Topic Properties there will be a "None" value in the Style Sheet field in the Appearance tab.
If you have this issue on multiple topics, you can use the Topics List pod - available from the View > Pods menu item - to multi-select files. From there right click to select the Topic Properties and assign the required CSS file.