Does Filezilla set the file modified date/time of the file to the remote file 
date/time each upload?  

If so it won't change if the file on disk has not changed since the last upload 
(the scenario you describe above "... but haven't saved it").

As Geany uses the modified date/time of the file to drive the reload query it 
won't see any change if the file date/time does not change.  But saving from 
another editor sets the modified date/time and triggers the query.

Nothing in the scenario touches the buffer in Geany, it is not connected to the 
file on disk, your magnum opus of "//1234" is still there, just save it.  In 
fact I would have thought the risk of losing it was increased if you get 
multiple reload queries, thats multiple chances to accidentally say "yes".

Kate may use another metric to indicate "changed" or maybe it uses the OS 
`inotify` facility.

But `inotify` (and therefore its Glib wrapper `g_file_monitor`) has limitations 
and bugs (described in `man inotify`) and although it was tried in Geany it was 
disabled because it missed changes, does not see files on remote filesystems, 
and doubled up reports of changes. 

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