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Hi Austin,
For each of the vertices that you are dropping, is there a difference in the number of edges connecting to them? When vertices are dropped in Neptune, any connecting edges have to be dropped as well. Edges cannot exists without vertices at either end.
We have a example implementation for a multi-threaded drop that maybe of use. It is written in Python, but you can port this to any language that supports some sort of threading/multiprocessing library: https://github.com/awslabs/amazon-neptune-tools/blob/master/drop-graph/drop-graph.py
The example's purpose is to drop an entire graph, but you could extend this to only drop a certain subset of a graph. To make this performant, the example fetches and deletes edges first as to not incur the additional penalty of querying for and deleting edges when deleting a vertex.
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