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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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