To reproduce:
- Enable the search row in the grid.
- Enter some text in the search text box in order to mark some rows.
- Refresh the master template.
- Notice that the text is cleared, but the formatting remains.

Workaround, use the following custom cell:

      class MyGridSearchCellElement : GridSearchCellElement
        {
            public MyGridSearchCellElement(GridViewColumn column, GridRowElement row)
                :base (column, row)
            {

            }
            bool performSearch = true;
            protected override void SyncLabelText()
            {
                //base.SyncLabelText();

                GridViewSearchRowInfo searchRow = this.RowInfo as GridViewSearchRowInfo;

                if (searchRow == null)
                {
                    return;
                }

                performSearch = false;

                string searchCriteria = typeof(GridViewSearchRowInfo).GetField("searchCriteria", BindingFlags.NonPublic | BindingFlags.Instance).GetValue(searchRow).ToString();

                if (string.IsNullOrEmpty(searchCriteria))
                {
                    this.SearchTextBox.Text = String.Empty;
                    this.SearchTextBox.SearchInfoLabel.Text = String.Empty;
                }
                else
                {
                    this.SearchTextBox.Text = searchCriteria;
                    this.SearchTextBox.SearchInfoLabel.Text = string.Format("{0} {1} {2}", searchRow.CurrentResultIndex + 1, Telerik.WinControls.UI.Localization.RadGridLocalizationProvider.CurrentProvider.GetLocalizedString(Telerik.WinControls.UI.Localization.RadGridStringId.SearchRowResultsOfLabel), searchRow.CurrentSearchResultsCount);
                }

                performSearch = true;
            }

            protected override void Search()
            {
                if (!performSearch)
                {
                    return;
                }

                base.Search();
            }
        }


To put it in action, use the CreateCell event of RadGridView:
 void radGridView1_CreateCell(object sender, GridViewCreateCellEventArgs e)
        {
            if (e.CellType == typeof( GridSearchCellElement))
            {
                e.CellElement = new MyGridSearchCellElement(e.Column, e.Row);
            }
        }