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How can I change that setting?

I want to upload files only if they are newer than the version in the FTP server.

Is there a reset setting options that I can use without erasing my FTP connection settings?

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up vote 6 down vote accepted

Yes, there is a setting that you can change. It is under Edit > Settings > Transfers > File Exists Action In your case you would change the setting that said "Uploads" to "Overwrite file if source file newer"

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In the latest version, this was changed to Transfer > Default File Exists Action

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