I deleted the geanygdb.html from the server manually. Without having studied the bunch of shell scripts here in deep, I assume it doesn't handle removed plugins at all.
While at it, I also updated the special handling of the renamed plugin (Geany)LaTeX in #11.
@frlan https://github.com/geany/geany-plugins/blob/master/latex/README contains to a broken link. You could update it to https://plugins.geany.org/latex/.