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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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"
In the latest version, this was changed to Transfer > Default File Exists Action
October 2017 - It is
Transfer Default File Exists Action
Then you can set it however you like.
BUT, your question is about the concern of overwriting the FTP connection settings.
And here's the rub: It does not save this setting in the FTP connection. It is session-wide, regardless of which connections you use, or how many are used before FileZilla is closed...
In other words, you have to set it every time you start FileZilla. If you forget and begin a transfer, you can change it while it is transferring, and wherever it is in the queue it will then begin using the new setting.
So your answer is that you do not need to worry about it resetting your FTP connection, nor its settings.