We might be better equipped to assist if you are able to better articulate what the exact problem is.
What you have described is not that different than arriving at a medical facility and shouting your leg hurts!
Okay, we know your leg area hurts, but does it hurt all the time? Only when standing? When walking?
So, does the TOC simply not appear for the merged projects? Or do you see it but clicking any links result in no activity? What exactly happens?
Same goes for the Index. Does the index even appear? If so, are the entries not working? What exactly is failing?
OK, so my post was just a summary really!
I have a main project with its own TOC, index and topics. I then have several other projects with their own TOCs, indexes and topics, and these are merged into the master TOC. In all these projects, we use the indexes to contain function ids for our software, so that when you press F1 in a software function, it invokes the correct Help topic in the CHM. The software is coded so that it goes to the main project first, and then looks in the merged index to find the link to the Help topic.
In the individual sub projects, the TOCs and indexes are present and work correctly. Also, in the master project, the TOC and index works correctly in the original English version. However, even though the TOCs, indexes and topics are all present and correct in the translated versions (Russian, for example) the index in the master project does not contain the entries for the sub projects. The TOCs for the sub projects do, however, work correctly.