Hi Dan,
The most likely cause here is duplicate topic IDs in your two projects. See this topic in the documentation for an explanation and mitigation strategies:
http://www.helpandmanual.com/help/index ... ar_ids.htm
Another question about this. Project B has a variable for the product name. Can I override that variable in project A so it automatically flows down to Project B? This way I can use Project B in multiple help files.
Absolutely: Since project A is the master project all changes there have priority. If the same variable is defined in the master and one of the children, changing it in the master will overload it in all the children where the same variable is defined. The only way to prevent the master version being used in a child would be to redefine it in individual topics using the topic variables feature in the Topic Options tab.
Note that this only applies to the master, i.e. the project into which the child is inserted. If you have two children in the same master, changing a variable definition in one of the children will have no effect on the definition in the other child. They are structurally side by side, and they can't pass any information to each other.