So after waiting for some time and not finding an answer I posted the same question to one the developers of the Beyond Compare team. He said its not possible in the current version. But there is a workaround for it.
What we can do is hardcode
the values of the folders that we don't need in the filter list and this will take care of it.
So for our example we can make a script like
filter "-SubfolderB\"
load c:\Folder1 c:\Folder2
sync update:left->right