Hello @Stvnly,
I hope you are doing well, and thanks for reaching out. We're sorry for the trouble you had. In Acrobat, when you use Window > New Window, both windows are actually two views of the same document instance, not fully independent copies. Because of this, some navigation actions (including bookmarks/left navigation panel) can stay linked between the views, which can lead to the behavior you’re seeing.
Does this happen with all sets of PDFs, or with any specific PDF? Assuming you are on the latest build of Acrobat version, and a Windows machine: 26.001.21677, Planned update, Jun 17, 2026, for testing purposes, go to Menu > Preferences > General
Uncheck “Open documents as new tabs in the same window”
Restart Acrobat
Open the same PDF twice from File Explorer (instead of New Window), and check the behaviour.
Also, capture exact reproduction details. Because this is intermittent, note which window had focus last, whether the bookmark panel was clicked in window 1 or window 2, and whether it happens right after switching focus between the windows. Please note that if the goal is to view two parts of the same file at once with independent navigation, use Window > Split instead of New Window. As with Split, "you can independently scroll, change the magnification level, or switch to a different page in the active pane without affecting the other pane." Use Window > Split for two panes; to return to a single pane, choose Window > Remove split. For more details, please check this article: https://adobe.ly/4wdCHFy
Let us know how it goes, and share your findings.
Regards,
Anand Sri.