Dmitry,
thanks for your intrest in our project and feature suggestions!
As I understand all your suggestions concern the multiple alignment editor. Here are some remarks:
Undo/Redo operations are available in MSAEditor. Check the buttons on the Toolbar
More details are in the documentation:
http://ugene.unipro.ru/manual/msaed_edit.html#undoUse "Save A Copy" option to save the modified document with another name. It works like "Save as". In the Project view right click on the document to choose this option. (See image attached)