The delete in the load Data section of the graph studio clears the whole graph. I think so it should not have deleted the data of other graphs but it is not meant to delete data from one vertex.
If you want to delete data from a single vertex instance, go to the explore mode -> search for that instance and delete it by selecting and clicking the trash button. If you want to delete all the data from a vertex, go to the gsql shell and use
USE GRAPH <graph_name>
delete from <vertex_name>
you can also use the where to delete a group of vertices from that vertex.
delete from <vertex_name> where
I haven’t found this operation in graph studio. Hope this helps.