The reason behind losing the links is that even after moving the Operations from an inner scope to an outer scope, the links starting from the moved Operations continue to belong to the inner scope. When the inner scope is deleted, all the links and Operations
in it are deleted as well, resulting in the behavior that you described. To avoid this, select the output links from the shapes as well before clicking 'Move to Working Scope'.
Map operations and links are now scoped. The inputs to a map operation belong to the scope of the map operation itself, and move together with the map operations. However, output links from a map operation can be used in that scope or any of the child scopes.
Hence they do not move with the source map operation.
However, when links connected to the target tree nodes are not in the same scope as the source map operation, the scope of that link is not visibly clear on the surface. This is a known issue. However, the properties window displays the parent scope of the
links correctly, and can help clarify the scope of the links in such scenarios.