The topology layout file is saved individually per local Prime LMS user. It's somewhere like: C:\Program Files (x86)\CSCOpx\campus\etc\users\admin\Layer~2~View.xml (on Windows, with the lowest directory level equal to the username. Soft appliance would be in ./opt/CSCOpx...)
There's no supported way of synchronizing them (although some folks have hacked it by syncing the files manually) and the file format is not documented. It is however, pretty simple-looking xml and one can easily inspect the file and see some of the high level constructs. There's also a user.preferences file that captures the overall preferences for Topology (layout type etc.). These files reflect the selection of options in the Topology menus and dragging objects and connections around and otherwise customizing the various views.
In any case, if one deletes things that are found (via subsequent discovery or data collection) to be in fact active, they will reappear and be placed according to the settings for the layout type (symmetric, orthogonal, etc.).
