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Certainly you can muck about with the behind the scenes files to influence things, but I would think it would be infinitely simpler to just modify the skin or the project in RoboHelp, then re-generate and re-publish.
Helpful and Handy Links
...just now revisiting the project that precipitated the original request. I have additional info and a request:
The separate help documents had been published without resetting the browse sequence. As it is today, (because browse sequences were not updated), many hyperlinks jump out of the published books and over to an earlier build that has a single TOC (same IIS server, but completely different path).
I learned that a RH HTML project can have multiple TOCs. So, my new question: is it possible for three TOCs to keep thier own browse sequences and access one common set of published HTM topics? How would that be engineered? I don't quite know how to manage hyperlinks that reference topics in one of the other books. I don't want to inherit the wrong browse sequences.
The alternative is to generate help from the 4 different TOCs into 4 different folders, which is a lot of replication. Like Siamese twins, there's a lot of cross sharing built into the original project, so in most cases, the "see also" relationships would give each separately published book 100% access to all the topics, but from a limited TOC.
It sounds like you think there is a link between the TOC and Browse Sequences. You can create one browse sequence based on one TOC but after that you create whatever you want.
Whilst RoboHelp allows a topic to be in more than one sequence, you have to be careful doing that. If your generated help includes a topic that is in two sequences and both of the next topics are also in that help, how does RoboHelp know which one to go to next.
Create a copy of your project and test using that.
See www.grainge.org for RoboHelp and Authoring tips