with 3 open panes ( +pdf annotating ) is hard to find best sizes of all panes, so i always working seconds maybe one minute on zoom-in and outing of those panes but i figured out that after opening my browser logseq app will resize itself to the default size. i found this out on 2 pc/laptop and on chrome/brave.
Can you please share a video or a GIF explaining what you mean?
Are you using the browser version or desktop app? BTW, the desktop app now supports multiple windows too.