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Putting files will overwrite files on the server unless your server settings are messed up.
One situation where that's not the case would be when you upload a file with a different CaSe StRucTuRe. Servers are case sensitive, so if you have a page locally, called index.html that you change and upload to the server, where the same page is called INDEX.HTML, it will load as a separate file. On the server, case structure differences are treated as separate files. On your local machine, a link to index.html or INDEX.html will go to the same file, you aren't allowed to have two with the same name, in the same directory,no matter what the case structure is.
Sometimes, the FTP won't replace the old file with a new one. I've encountered this a few times both in DW and FileZilla (a 3rd party FTP Client). I found that physically deleting the old file from remote server and then uploading new one did the trick.
So it does replace the file unless there's a glitch, Thank you!
I've rarely experienced the problem that Nancy mentions, and yes, definitely putting the file will overwrite any existing file with the same name.