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Are you automatically creating the TOC? Even if you were, unless there is a topic inside the folder I'd be totally surprised if it was listed there.
The bottom line is that RoboHelp believes there is content inside the folder that is still being used. This means you have a reference somewhere inside a topic pointing to something inside the folder. Might be an image, CSS file or something else.
Once you figure out what that something is, you are able to kill the reference and finally delete the folder from RoboHelp.
Thank you so much for the quick reply. I will look into it.
Ok, now I have solved the mystery how this project sub folder was created. I had created this out of the Project Manager, in RoboScreenCapture tool and had saved some images in this sub folder. I deleted all those images in RoboScreenCapture tool and then deleted that sub folder. However, if I come back to Project Manager, I still see this sub folder there. I don’t know what to do?
You should never delete files or folders using anything other than RoboHelp. As I said earlier, the reason you see the folder and the delete option isn't available is because RoboHelp believes it is in use. This means you have probably inserted the image(s) in a topic(s). By deleting the images from the folder using RoboScreenCapture or Windows Explorer, you have introduced missing image(s) in a topic. That's bad news.
You can probably figure out where the references are by looking at the images pseudo folder in the project manager. The missing images should be listed with a red X. You could then right-click the image and inspect the Properties to determine which topics are expecting to use the image. Once you have that info, you are able to edit the topic(s) and kill the references. Once all references are gone the delete option for the folder should be available from RoboHelp.