Are you using an external text editor, if so which application?
It sounds to me like perhaps FlashFXP is not detecting the local temporary file was modified.
If you are not using an external editor I would recommend it and see if that resolves the problem.
You might also try clearing your active edits list if you haven't already done so.
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I also notice that clicking "Open folder location" and "ReDownload" in that same menu does nothing. "Auto upload on change" is checked.
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I am not quite sure what to make of this, I will need to investigate the issue further.
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For "Legacy Prompt," the "Confirm" window is modal and I can't interact with the editor until I close it.
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Thank you, I have determined that is a logic flaw when using the legacy prompt with the built-in editor.