Row indexes which no longer exist are removed from selectedRowIndexes.

AppKit/CPTableView.j

@@ -1500,8 +1500,19 @@ CPTableViewFirstColumnOnlyAutoresizingStyle = 5;
 
 - (void)noteNumberOfRowsChanged
 {
+    var oldNumberOfRows = _numberOfRows;
+
     _numberOfRows = [_dataSource numberOfRowsInTableView:self];
 
+    // remove row indexes from the selection if they no longer exist
+    var hangingSelections = oldNumberOfRows - _numberOfRows;
+
+    if (hangingSelections > 0)
+    {
+        [_selectedRowIndexes removeIndexesInRange:CPMakeRange(_numberOfRows, hangingSelections)];
+        [self _noteSelectionDidChange];
+    }
+
     [self tile];
 }