Fix T102329: Update cache of node tree topology after all link changes for valide cut checking

In 8da253cfb64f the state of the link owner node is checked by node_link_is_hidden_or_dimmed.
Due to the fact that the deletion of links occurs immediately after
the check and in order, after each deletion, need to update the geometry cache.

Possible also first check all links to delete, and then delete.
In theory this should be more efficient. If this variant is considered better, the patch may be revised.