From OpenSCADAWiki
Changing of some node's configuration will set the modification flag for the node, and also will set to active for buttons "Load from DB", for loading the initial configuration, and "Save to DB" for the changes saving. The modification flag also rises to parent node, which allows to restore-save from the root node, but really into the operations with DB will participate only modified nodes. 
A node removing causes to removing it from the storage and the modification mechanism does not work for this operation.