What do you mean by the "Replicates window"?
I do not think I understand what you are saying is happening. I am not seeing anything like that when I try Ctrl + Up / Down in my documents.

Could you post a screenshot?
I also might need to see your Skyline document. I suspect that this might have something to do with the arrangement of your chromatogram graphs. If you send us a .sky.zip, it will include the .sky.view file which specifies the layout of the chromatogram graphs which might be necessary to reproduce the behavior your are seeing.
-- Nick

Thank you for sending me your Skyline documents.
I see that you have 130 replicates.

Skyline never allows you to have more than 100 chromatogram windows displayed at the same time. This includes chromatogram windows that are actually visible, and chromatogram windows that are hidden on inactive tabs. If you already have 100 chromatogram windows displayed and you try to display a new one, Skyline finds the chromatogram window which was last active the longest time ago, and repurposes that window for the new replicate. For this reason, if you linearly navigate through all 130 of your replicates, when you get to the end, the last 30 replicates will be displayed in the places that the first 30 replicates originally were.

At the time that we implemented this limit, we thought that maybe in the future we would need to add a configurable setting somewhere so that users would be able to control the exact value of this limit.
We added the limit in 2019 because a user had 1700 replicates in their document and Skyline was running into the User Process Handle Quota which by default is set to 10,000.

It would not be difficult to add a setting for this. We would probably put a text box somewhere on "Tools > Options".
-- Nick