FlashFXP provides two ways to edit files, If you want to edit the file remotely you can right-click and select edit, this will launch the windows default editor for the file type (Default editors can be customized via Options > File Associations)
If you want to edit the file locally and then upload it this can be done via right-click Advanced Transfers > Edit & Upload.
By default after you're done editing the file and click save in your editor the file will be automatically uploaded to the server. This can be configured to prompt or manual upload via Options > Preferences > View and Edit File > Default action on save.
These are the preferred method of editing files in FlashFXP.
If you prefer to edit the file some other way and then manually upload it and if you have the file accidentally queued for download with your file transfer rules set to overwrite this could cause a major headache. I understand that this is human error and we all make mistakes but I'm not entirely sure there is a viable way to prevent or warn the user in such a situation. All of the methods that come to mind would add significant overhead and be quite inefficient.
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