We did set a limit of 100 active panes in 20.1, because the package that manages the panes eventually experiences performance issues with this number unbounded. For one, it consumes windows handles for every pane and it can actually run the system up to its handle limit and that kills Skyline.
You can, however, still view all 200 replicates in your document. It is just that when you do something to activate a replicate which does not currently have an assigned pane, Skyline will assign it a pane, I think replacing the least recently used pane. You should be able to see this in action, but clicking on a replicate in any of the replicate summary graph panes (e.g. Retention Times: or Peak Areas: Replicate Comparison) or by using the "Replicates" dropdown list in the Targets view, or by using Ctrl-Up or Ctrl-Down to cycle through the replicates in your document. Or by clicking a replicate link in either the Document Grid or the Results Grid.
Hope this helps. The maximum 100 visible panes is an effort to address a real issue. It was our belief that the tabbed UI becomes extremely cumbersome anyway with that many active panes, and that users were more likely to rely on the UI elements I have listed above for navigating their replicates.
Hope this helps. Thanks for your feedback.