Sorry you lost your file, but this is a known situation.

There are several options that control how Geany saves files, see [this](https://wiki.geany.org/config/all_you_never_wanted_to_know_about_file_saving).

Several of the options are known to have problems on full file systems (see the article) and are likely to result in loss of the original file, but these options have advantages in other situations, so its a trade off and makes it difficult to decide which is chosen as the default. The default value works best in normal operation, so its the default, but as that article notes, its is a system library and has a bug which has been known for a very long time and looks like it will never be fixed. Sadly that bug destroys the original file if the save fails.

And also note the initial paragraphs of the wiki article, so long as Geany is not closed you still have the buffer in memory, so you can save the buffer that is still in Geany somewhere else when a save fails.