You need to "lock" the vertices in their current locations, which will prevent them from being moved the next time the graph is refreshed. Here is one way to do that:
1. Right click the graph pane.
2. In the right-click menu, select Select All, Vertices.
3. Click the "lock" icon at the top of the graph pane. The icon might be hidden under a "down arrow" if the graph pane is narrow.