This appears to be a bug. We'll have to get it fixed.
In the meantime, probably the simplest thing to do to avoid the hassle losing your basestyles is to copy the generated code into a new method and call that method from a FormLoad handler. This means the code will be hit even if it gets zapped from the generated code. Of course this makes using the designer for basestyles not optimal. But if your basestyles are more or less static, then this work around may be usualble until we can fix this is a release.
To give you an idea of what I mean, I just changed the BackColor of the Header basestyle. From the designer generated code, I copied these two code blocks into a separate method that I called from the FormLoad to guarantee my modified basestyles were used.
//first code block
Syncfusion.Windows.Forms.Grid.GridBaseStyle gridBaseStyle1 = new Syncfusion.Windows.Forms.Grid.GridBaseStyle();
Syncfusion.Windows.Forms.Grid.GridBaseStyle gridBaseStyle2 = new Syncfusion.Windows.Forms.Grid.GridBaseStyle();
Syncfusion.Windows.Forms.Grid.GridBaseStyle gridBaseStyle3 = new Syncfusion.Windows.Forms.Grid.GridBaseStyle();
Syncfusion.Windows.Forms.Grid.GridBaseStyle gridBaseStyle4 = new Syncfusion.Windows.Forms.Grid.GridBaseStyle();
//second code block
gridBaseStyle1.Name = "Header";
gridBaseStyle1.StyleInfo.Borders.Bottom = new Syncfusion.Windows.Forms.Grid.GridBorder(Syncfusion.Windows.Forms.Grid.GridBorderStyle.None);
gridBaseStyle1.StyleInfo.Borders.Left = new Syncfusion.Windows.Forms.Grid.GridBorder(Syncfusion.Windows.Forms.Grid.GridBorderStyle.None);
gridBaseStyle1.StyleInfo.Borders.Right = new Syncfusion.Windows.Forms.Grid.GridBorder(Syncfusion.Windows.Forms.Grid.GridBorderStyle.None);
gridBaseStyle1.StyleInfo.Borders.Top = new Syncfusion.Windows.Forms.Grid.GridBorder(Syncfusion.Windows.Forms.Grid.GridBorderStyle.None);
gridBaseStyle1.StyleInfo.CellType = "Header";
gridBaseStyle1.StyleInfo.Font.Bold = true;
gridBaseStyle1.StyleInfo.Interior = new Syncfusion.Drawing.BrushInfo(System.Drawing.Color.FromArgb(((System.Byte)(255)), ((System.Byte)(192)), ((System.Byte)(192))));
gridBaseStyle1.StyleInfo.VerticalAlignment = Syncfusion.Windows.Forms.Grid.GridVerticalAlignment.Middle;
gridBaseStyle2.Name = "Column Header";
gridBaseStyle2.StyleInfo.BaseStyle = "Header";
gridBaseStyle2.StyleInfo.CellType = "ColumnHeaderCell";
gridBaseStyle2.StyleInfo.Enabled = false;
gridBaseStyle2.StyleInfo.Font.Bold = false;
gridBaseStyle2.StyleInfo.HorizontalAlignment = Syncfusion.Windows.Forms.Grid.GridHorizontalAlignment.Center;
gridBaseStyle3.Name = "Row Header";
gridBaseStyle3.StyleInfo.BaseStyle = "Header";
gridBaseStyle3.StyleInfo.CellType = "RowHeaderCell";
gridBaseStyle3.StyleInfo.Enabled = true;
gridBaseStyle3.StyleInfo.HorizontalAlignment = Syncfusion.Windows.Forms.Grid.GridHorizontalAlignment.Left;
gridBaseStyle4.Name = "Standard";
gridBaseStyle4.StyleInfo.CheckBoxOptions.CheckedValue = "True";
gridBaseStyle4.StyleInfo.CheckBoxOptions.UncheckedValue = "False";
gridBaseStyle4.StyleInfo.Interior = new Syncfusion.Drawing.BrushInfo(System.Drawing.SystemColors.Window);
this.gridDataBoundGrid1.BaseStylesMap.AddRange(new Syncfusion.Windows.Forms.Grid.GridBaseStyle[] { gridBaseStyle1,
gridBaseStyle2,
gridBaseStyle3,
gridBaseStyle4});