i was just bitten quite badly by a geany behaviour and wanted to warn other users about it...
The project files use absolute paths. That just let to me inadvertently editing html/php files on a live webserver, when i _thought_ i was editing those under my home directly (because that's where i opened the project file from). When none of my changes were appearing in my browser, i started poking around and found that i was editing files under /var/www/... instead of under ~/public_html, even though my project file was opened from ~/public_html. (Yes, my account has write access to /var/www/..., though that would normally not be the case and the error would have shown up when i tapped Ctrl-S.)
So... when you have a project file checked into your source control and you check it out two times on the same system (under different paths), then be damned sure to modify them to have the correct paths (and not check it in, or you break the other one). And make damned sure your coworkers who also use that project file do the same.