I get the reload indicator if ./tempdir/file1 is more recent than ./file1 (and ./file1 is open in Geany).
Isn't that the situation with your reproduce instructions in the OP, `temp/file1` is created after `./file1`? Which is why it worked for me.
If its the other way around and the file manager copies the date/time from the older file to the newer file during a copy then yes there is no prompt because [the compare](https://github.com/geany/geany/blob/11436f58defe5312c4d6eec1225868c5dca585e4...) is `<` not just `!=`. Its been that way for at least the 10 years I looked back before I got bored. And the info message does say "file on disk is newer" so I would say its intentional, the code is looking for a file that has been modified after it was last saved, so its mtime should be newer.
File managers backdating the modification time on changed files is a "bad thing" because if it does that to a source code file then `make` will break when next run :cry: .
Plain `cp` of course sets the mtime to now, not the from file time, when it does the copy so you get the message.