You can follow these steps :
1) Open RobohelpHTML and double click on the output which you want to generate from RHCL (Launch Robohelp HTML 9 -> Under Single Source Layout Pod -> Double Click on WebHelp)
2) Webhelp Settings window will appear, under Content Categories choose your Default content
3) Choose your Index & TOC from Drop Down Menu and save the changes
4) Generate WebHelp output from RHCL command, TOC and Index should appear this time
Note : Assuming you are generating WebHelp
Hope this helps !!
Yes, that did it. Thanks!!
Can I ask why this is picked up from the SSL, but not when I've marked my created index/toc as default in the project manager?
When you generate WebHelp ouput from RHCL command, it check for TOC and Index which are saved on the SSL.
I got this same issue, about 6 months ago and what I found that when "default" is selected for TOC and Index, RHCL does not pick that and when you manually select your TOC, Index and save it, RHCL picks that.