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Publishing takes files that have changed (newer time stamp) and copies them to the destination folder (in this case, your network folder).
Applying conditional tags to topics (at either the topic or content level) is a change to the topics, and publishing without the Republish All option should copy those changed files to the network folder. The copied (newer) files overwrite files of the same name in the network folder.
Any files you didn't change will not be overwritten on the network unless you do "Republish All."
So what type of scenario would prompt you to check the 'Republish all' box. It is my understanding from your response that I do not need to check republish all when I add conditional build tags because the corresponding topic, being changed, will update accordingly in the network folder. Am I following?
I imagine that one scenario would be that some problem begins occurring with the files on the network and you're not able to figure out what's wrong. Republish All would allow you to overwrite all files and thereby refresh the help in its entirety.
Ben's reply is a good one. But just in case that you mentally didn't connect with that situation, I'll toss out another where you might want to check the Republish All option.
Back when I was working in the corporate world, on more than one occasion I arrived to work on a Monday to find a nice little note from my network admins. Generally it would go a bit like this:
Unfortunately, during the process of (insert situation here - Upgrade, Backup, Migration) of the servers over the weekend, things went dreadfully wrong. We believe we have restored all the files properly from our backups, but please double-check your links to ensure all is well.
So, in this situation, do you think I'm going to waste my time "checking links"? Heck no! I'll be checking that Republish All option and be done with it.