It is nice to see the addition of Link Charts to 2.6. I created two sets of links with a set of blue lines and a set of green lines. When I select Display Links on Map, the map only shows the green lines. Is this a software limitation, (ie. only show one set of lines on the map), or a user that doesn't know what they are doing?
This screen shot show the Link Chart with the 2 sets of lines. The map (not shown) only shows the green lines.
Also, I found that if your first set of entities and relationships are in one projection (in my case the map frame was in this projection too), and you add another entity and relationship that is in a different projection, Pro will crash when you either select Display Links on Map or click on the map tab.
In case you hadn't see it yet, here is the Link Chart Ribbon
The answer is yes. First one link disappeared from the map after only being seen for a very short time. Then the second link in the map disappeared. And they would not come back. Without knowing if the links could be redrawn I created a new link chart and both lines are showing up. I did not read the documentation very thoroughly but I wonder how it knows which map frame to draw the lines or if there is a process to tell it to draw the link in this map frame versus another map frame.