I have the layer that refreshes periodically, and I've noticed that once I have the popup opened, then its content goes blank, though it still contains some data (features).
So I've tried to implement something that will grab the last ObjectID and after refresh to find it in the data and set the popup features object to that particular feature, but it doesn't appear to be working. See the sample
In the sample above, the featurelayer refreshes every 5 seconds. You can clearly see how the popup behaves.
Then un-comment last few lines in the that set the popup features parameter to new feature. It seems like it's unable to render it or something else.