<blockquote>
<p>I did mention the files are opened via sftp in nautilus on Ubuntu 16.04.</p>
</blockquote>
<p>Thats not prescriptive, it could be GVFS, FUSE or sftpfs.</p>
<p>Gedit is known to use gvfs internally, but there was insufficient interest by anyone capable of testing it for a PR adding it to be included in Geany, and the PR is now well out of date.</p>
<p>As I said Geany only opens local files, so Nautilus must set up a FUSE or sftpfs mount for Geany when you open the file.  Check the settings for whatever mechanism it uses and see if they cause the problem.</p>
<p>I don't know what vim and atom do thats different, you could look and see.</p>

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