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A few things you could try:
Try running Geany from the command line like geany -v and then changing the theme and exiting Geany as you normally do. Take note of the messages printed to the terminal and paste them here.
Try setting the theme and closing Geany using File->Quit, just in case the window manager is doing something weird and killing Geany or making it crash.
Try running Geany from the command line, specifying a different configuration directory, in case there is something wonky with your default one, like this geany -v /tmp/geany-test-config. Change the theme and exit normally and re-open to see if the setting was saved.
With no instances of Geany running, make a copy of the file ~/.config/geany/geany.conf to somewhere else, open Geany, change the theme, and exit normally. Make another copy of that same file, and compare them manually, using diff, or your favourite compare tool.
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