I can't reproduce my own report. But it happened once. And I made a screenshot. And it happened always when I was using Geany 1.39 by PPA with the plugin Geany Preview and with two lua-scripts.
I can't reproduce https://github.com/geany/geany/issues/2559, because in my case in the moment where line numbers are visible, then the issue does not exist. I can't reproduce https://github.com/geany/geany/issues/1521. And I can't confirm the description. In my case the issue didn't happen when I was typing. The issue appeared when I was scrolling.
If you can confirm it with Geany git version or latest Scite then please report to Scintilla referencing this issue.
I don't know how to install Geany git version or latest Scite. But I will report it to Scintilla.