Lots of things don't work in split window, just search issues. That will also give you discussions about the various attempts to fix it. ATM split windows should really be seen as a read only window, even if basic editing works because the Scintilla edit does it.
tl;dr fixing it is a lot of work as most of Geany is coded on the assumption of only one editing window, and no plugin can change that, so "somebody" has to make the changes
Search will also show the various ways attempts have been made to fudge it with varying success, but never good enough to keep.