@arigit Geany hasn't changed, so it sounds like Fedora has. It sounds like it does not keep the SFTP mount open after Nautilus has mounted it? First thing to look at is the release notes on Fedora for Nautilus, SFTP and general and see what is listed as changed.
I am not aware of any of the Geany contributors using Fedora and SFTP so you probably will have to do the evaluation.