It sounds like you have published the help and pointed the publishing folder to the folder containing the source files. So now what you have is source files mixed up with output files, or put another way, an unholy mess.
Hopefully you have a backup taken not too far back.
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In addition to what my esteemed colleague advised, I'll also add this. The use lower case file names option should never break anything. In fact, it helps matters. Here's why.
Perhaps you have a topic you created and you named it MyTopic.htm. You have many different files and folders and instead of using the dialogs or drag and drop to link things, you just type mytopic.htm. (note the difference. MyTopic.htm vs mytopic.htm)
If you generated without the user lowercase option and published to a Windows web server, the link would still work just dandy because Windows doesn't consider mytopic.htm to be different from MyTopic.htm. In fact, you cannot have two files named that way on Windows. To Windows it's the same file. But if your server is UNIX or LINUX based, it's very persnickety that way and the link will fail.
Since Windows doesn't care about case but 'NIX does, I always suggest folks use that option when they generate, because you sometimes can't be sure which variant of web server you have.
Additionally, during the generation process, any links that are case mismatched are corrected, because it's all converted to lower case. File names as well as any links in files.
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