To answer your second question, the chapters are not stored in RTF files. For each scene there is one in the old yw5 format, but the chapter structure is stored in the .yw5 file. If you simply delete individual files, you will damage your project. It is safer to use the new yw7 format, where the entire project is in a single file.
I can definitely recommend you to upgrade to yWriter 7 and convert your projects to the yWriter7 format:
Main menu > Project > Project Settings > Misc Settings
Cheers,
Peter