Teleporters lose their linked status upon using undo.
This occurs on all teleporter types.
Neolemmix editor V1.14
Undo is very buggy in general. For example, sometimes if you make a change to the stats / skillset then a change to the layout, hitting Undo a single time will revert both.
This is something I need to look into, but so far I'm not even sure how Undo works in this editor, let alone how it might be fixed.
Not sure exactly when this was fixed, but it no longer happens in the latest code.