I'm unable to remove a folder from the Project Manager pod as the Delete button is disabled. To remove the topics that are listed under a book, I've removed the book from the ToC, manually deleted the folder on the machine, deleted the topics from the Topics List pod.
The topics aren't there in the ToC, but, when I click certain index entries, it takes me to those deleted topics.
I've also deleted the .CPD file and after generating the output (.CHM), the topics are displayed when I click the specific index entry.
Not being able to delete in Classic indicates that RH believes there are files in use in the folder. Deleting the topics from the TOC will not delete them from the project. You need to delete them from the folder in the project manager pod to delete them from the project.
You said you deleted the files using File Explorer and I'd expect that to mess up your project. So I'm a little confused about how you can generate and have the files in the chm.
Do you have a recent backup of your project? If so, I'd recommend restoring a copy of the backup to a new location and deleting the files through RH (from the folder in the Project Manager pod). Don't delete your current project though, in case we need that content. (A new zip backup of the project folder wouldn't hurt, just in case.)
If you don't have a backup, then we might need to take a step back and assess what state your project is in before working out what the next steps are.