It's right that with synchronized scrolling enabled both panes of the split document window scroll instead of just the active pane.
I think, you are the first user using Windows - Synchronized Scrolling with 2 files side by side and with a split document window. Report this issue by email to IDM support.
There is currently no possibility to get a part of a file displayed fixed while using synchronized scrolling on another part of a file.
Of course with Windows - Synchronized Scrolling being disabled it is no problem to get first line displayed fixed at top while scrolling in second pane of a split document window. To split a document window click with left mouse button on the small rectangle above upper arrow on vertical scroll bar (mouse pointer changes to 2 thin horizontal lines with an up and down arrow) and drag down the horizontal line appearing across the document window.
On the other hand synchronized scrolling of upper and lower pane of a split document window can be very useful. For example when comparing within a C/C++ file two similar functions as I currently do. (Really!) So the problem with synchronized scrolling option is that it should be better managed. Synchronized scrolled can be used for comparing 2 files side by side and for comparing two blocks within same file. So perhaps 2 synchronized scrolling settings for the two uses cases would be better.