Assuming I'm understanding the situation correctly, you should be able to achieve it easily.
For starters, don't use the Global Breadcrumbs feature in the Single Source Layouts and only apply them selectively via Master Pages.
Use a different Master Page (or no Master Page at all) for the one topic where you don't want the breadcrumbs. Then add breadcrumbs to the master page and associate it with topics where you want breadcrumbs.
Helpful and Handy Links
When I create breadcrumbs through the WebHelp Navigation – WebHelp dialog box, then breadcrumbs are created on top of the HTML header. In other case, when breadcrumbs are created through master page, breadcrumbs are created below the header.
So, could you let me know that through master page how to bring the breadcrumbs above the header?
Ohhh.. I think Im close to my own question. I didn’t use header, instead of that I used a simple text in the master page, which I used it as a header for the HTML files.