I think the Scite version matches the Scintilla version, so 3.6.0, and Geany 1.27 uses 3.6.3 IIUC. Not a big difference.
What filetype is your file?
With current Git Geany I can use the down arrow key anywhere in a text file of 3 million+ lines. I do observe it gets slower the further down I get, but it never stops.