Yes, I know what you mean, you only lose the sync data if you delete the whole content of the meta event.
But still, I think if you have a visual feedback about where this data is within the lyrics, it is easier to edit them without losing sync.
Maybe this could be an on/off option - to show or not to show the data in Edit mode. When it is set to on and you enter Edit mode, you could see a symbol which shows where the meta event starts, like for example the circle symbol I used above.
Alternatively, the Edit window could include the Sync window and when you move the cursor and modify data in any of the windows, the changes are reflected in the other one too.