RiffRaff;I'm not sure I follow you.
There can only be one "Source" folder for each project and the "Source" folder must not contain any additional folders.
To prevent any confusion, about using index files with HYPrLock. follow this procedure.
Create and name a Project folder for your new eBook - Inside that project folder create "Source" and "Output" folders. These you will use to create your eBook.
For example:
Project folder = "MyStory Project"
/ Output folder*contains your original "exe" eBook
/ Source folder *contains all of your eBook files.
HYPrLock "Turn Key" Project folder = "myProject"
/Output folder *contains your HYPrLock protected "exe" eBook
/Source folder *contains all of your eBook files + HYPrLock files
Always complete, build and test your Activ EBook before you ever consider using HYPrLock. Remember that HYPrLock is a security system for your eBook not part of the eBook itself.
After you have completed, built, and tested your eBook, change the name of your index file (i.e. index.html = index2.html) and move all of your eBook files from your Project "Source" folder to the HYPrLock (Turn Key) "Source" folder.
Finally, follow the HYPrLock instructions to finish your project.
Ron