I cannot catch exact steps to replicate that, but intensive editing with Undo/Redo operations and when there are objects with the same names ends with empty xmi file. Teiid Model Explorer shows nothing under model node,

New Child menu is empty on model node. Diagram meantime has "leftover" objects.

Another problem with Undo/Redo is sometimes it just stop react on assigned key combinations Ctrl-Z/Ctrl-Y

There are no errors reported in log.