Given that RH 9 is only capable of running on Windows, the "Use Lowercase File Names..." checkbox (see image below) can cause some unexpected issues when generating output for a unix (or linux) platform. I found this out recently when generating web output for a project that is being viewed on a linux platform machine and encountered hundreds of broken help links unexpectedly.
If this is the first time you are generating output from your project, this function works fine - it converts all topics, image files, and anything else needed to view the help, to lower case letters. However, if for some reason, you had generated previous outputs without checking this box, and now you decided that you want all of your output files in lower case, just checking this check box and regenerating the output won't work.
The reason is simple - the Windows OS does not distinguish between upper and lower case letters in file names (e.g., filename.htm is the same as FILENAME.HTM). Unix (and linux) are case sensitive, and treat those files are two distinct files. Consequently, RH does not (can not) change existing file names in your output folder with this checkbox checked, and gives no message indicating of such when generating the output. In this case, the only way to fix this problem is to clear out the folder containing your output files and have RH regenerate your project from scratch.
I had an additional issue that made things even worse. In one project for a linux platform, I must have unchecked this check box during project creation by accident (maybe over a period of days or weeks). Then, because of another issue, I needed to restore my project to an earlier stage. At that point, I found out that my help links needed files using both lower case and upper case file names for everything to work fine.
I didn't see any mention of this in RH documentation, so I thought I should alert the RH community.
If you are talking about the folder on the server you publish to, I totally understand. But if you are talking about the output folder of RoboHelp, I'm confused because the first step of generating WebHelp is to empty the folder in preparation for the new files.
My guess is that you are talking about the folder you Publish to. That's entirely different than the output folder. The publishing operation should not ever delete files.
Helpful and Handy Links
Yes - just to clarify, I am taking about the folder I Publish to.
Recap - Just warning those that publish to a Unix/Linux environment that if you need to change the case of file names in your folder that you publish to, and you've got stuff in there with the same name already, you'll have to delete the files first before republishing.