Geany currently constantly updates `.geany` project files with no option to choose in which state to save the session (and consequently also have an ability for project-wise presets/defaults). This is leading to issues such as #2304 and #2863.
This is a feature request for additional global option under `Preferences > General > Miscellaneous > Projects` so one can disable session autosaving and also add a manual option to do so, probably something along the lines of `File > Save Project`.
Also: Another option in the category _Use project-based session files_ disables using `.geany` files altogether and is not helpful in the case.