Please note the https://github.com/geany/geany/blob/master/scripts/update-scintilla.sh script which makes the update quite easy.
But please note that script also updates lexilla lexers where the real work is.
You have to check the mappings from Scintilla lexers to Geany highlighting in https://github.com/geany/geany/blob/master/src/highlightingmappings.h for every language that has a change to its lexer since the last version in Geany.