Not all links are preserved in the Tranquility view. However, if a link that is part of the "main body of text" is no longer visible, then please provide an example and I can take a look to see if this is a bug or a limitation/feature.

Some of the links (related to the article, but not part of the main article) may be preserved under the "More Links" menu. To access this, click on the (+) control at the bottom right corner of the screen and then on the "More Links" button. That should give you any related links that are captured. Note that this list will not include any links that are already part of the main article (as hyperlinked text).