Ant colony optimization for traveling salesman problem with changing graph-nodes/vertices
Yes, there are several papers on this topic, and related ones, in the context of ant colony optimization algorithms for routing on ad hoc or mobile area networks (MANETs).  In a MANET, the nodes in the network graph are mobile, and if they move too far away from their neighbors, they fall out of range, hence the communication link is broken (i.e., the edge disappears from the network graph).  The routing problem essentially is: how do I keep all the vertices connected, and maintain efficient pathways between nodes, when links can disappear and reappear?  Of course, if a node moves out of range from all other nodes, it is the same as if the node were deleted from the network graph.

The paper An ant colony optimization routing based on robustness for ad hoc networks with GPSs  by Kadono et al. contains a "related work" section you will probably find interesting.  In this paper I've linked, there is an assumption of the availability of some GPS information, which probably does not apply to you; I chose it mainly for its discussion of other papers.  However, all these approaches assume something about how nodes can be deleted (or suddenly appear), in order to construct an efficient algorithm.  You'll have to decide what formal assumptions hold for the problem you are trying to solve.

Search phrases like "ant colony optimization MANET" or "ant colony optimization self-stabilization" may turn up other papers of interest to you.