ftp publish uploads unnecessary files

Time how long it takes with and without Republish All selected. You may find there isn't a difference. Some time back I posted a bug to that effect.

I would be interested to know if you find any difference.

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My site www.grainge.org includes many free Authoring and RoboHelp resources that may be of help.

Regarding what's published, there will always be more files uploaded than you changed, because generating will update a lot of behind-the-scenes files, like the files that make search work. However, for more explanation of what gets changed, and to determine if there is a bug, you'll need to contact Adobe support using the email address here: https://helpx.adobe.com/contact/enterprise-support.other.html#robohelp

For the publishing issue, you could check with your IT people if it may be related to network glitches or timeout periods set on the server you're uploading to.  I'm pretty sure most will boot a connection if it's taking too long to transfer files for some reason (like a network glitch).