Hello Vasiliy,
there should be no problem with your approach (the extra content of the config file will be preserved by Geany).
However, Geany offers plugins the possibility to read/write from/to the project config files natively. When you register for the "project-open" signal, the callback is invoked every time a project is opened and you receive GKeyFile * config as a parameter from which you can read the configuration using
Similarly, when you register for "project-save", you can write your configuration to the GKeyFile signal parameter. You can also force the emission of the "project-save" signal by calling project_write_config().
You can check my projectorganizer plugin to see how to use the signals (the signals are registered in prjorg-main.c). You can also check
Cheers,
Jiri