Are you saying that if you use the `Document->Line Wrapping` menu item to enable Line Wrapping that it does take effect for any file except for `.bashrc` file? Or are you saying that `Line Wrapping` setting is not remembered for `.bashrc`?
I'm not sure if it will help, but you could try to delete the `[files]` section from `~/.config/geany/geany.conf` using a different non-Geany text editor, while Geany is closed.