In specification is written:

public void setRowSorter(RowSorter sorter)

    Sets the RowSorter. RowSorter is used to provide sorting and filtering to a JTable.

    This method *clears the selection* and resets any variable row heights.

    If the underlying model of the RowSorter differs from that of this JTable undefined behavior will result.

    Parameters:
        sorter - the RowSorter; null turns sorting off

But when I run the folloving code:

import javax.swing.table.DefaultTableModel;
import javax.swing.table.TableRowSorter;
import javax.swing.table.TableModel;
import javax.swing.JTable;
import javax.swing.RowSorter;
import java.util.Arrays;

public class Test1 {

public static void main(String argv[]) {
Test1 test = new Test1();
test.setGetRowSorterTest();
}

private int[][] rowsToSelect =
{
{0, 2, 4},
{0},
{0, 1, 2, 3, 4},
{3, 4}
};

private void selectRows(int[] rowsToSelect, JTable table) {
table.setColumnSelectionAllowed(false);
table.changeSelection(rowsToSelect[0], 0, false, false);
for (int i = 1; i < rowsToSelect.length; i++) {
table.changeSelection(rowsToSelect[i], 0, true, false);
}
}

private void prinSelectedRows(JTable table, String ms) {
System.out.println(ms + ": table.getSelectedRows() = " + Arrays.toString(table.getSelectedRows()));
}

public void setGetRowSorterTest() {
TableModel model = new DefaultTableModel(5, 3);
JTable table = new JTable(model);
RowSorter[] rowSorters = {
new TableRowSorter(model),
null,
new TableRowSorter(),
};
for (int i = 0; i < rowSorters.length; i++) {
for (int[] selectedRows : rowsToSelect) {

selectRows(selectedRows, table);
System.out.println("rowsToSelect = " +
Arrays.toString(selectedRows) +
"; Sorter = " + rowSorters[i]);
prinSelectedRows(table, "BEFORE");
table.setRowSorter(rowSorters[i]);
prinSelectedRows(table, "AFTER");
}
}
}
}
-----------------------------
 I get the output:
-----------------------------
rowsToSelect = [0, 2, 4]; Sorter = javax.swing.table.TableRowSorter@901887
BEFORE: table.getSelectedRows() = [0, 2, 4]
AFTER: table.getSelectedRows() = [1, 2, 3, 4]
rowsToSelect = [0]; Sorter = javax.swing.table.TableRowSorter@901887
BEFORE: table.getSelectedRows() = [0]
AFTER: table.getSelectedRows() = []
rowsToSelect = [0, 1, 2, 3, 4]; Sorter = javax.swing.table.TableRowSorter@901887
BEFORE: table.getSelectedRows() = [0, 1, 2, 3, 4]
AFTER: table.getSelectedRows() = [1, 2, 3, 4]
rowsToSelect = [3, 4]; Sorter = javax.swing.table.TableRowSorter@901887
BEFORE: table.getSelectedRows() = [3, 4]
AFTER: table.getSelectedRows() = [1, 2, 3, 4]
rowsToSelect = [0, 2, 4]; Sorter = null
BEFORE: table.getSelectedRows() = [0, 2, 4]
AFTER: table.getSelectedRows() = [1, 2, 3, 4]
rowsToSelect = [0]; Sorter = null
BEFORE: table.getSelectedRows() = [0]
AFTER: table.getSelectedRows() = []
rowsToSelect = [0, 1, 2, 3, 4]; Sorter = null
BEFORE: table.getSelectedRows() = [0, 1, 2, 3, 4]
AFTER: table.getSelectedRows() = [1, 2, 3, 4]
rowsToSelect = [3, 4]; Sorter = null
BEFORE: table.getSelectedRows() = [3, 4]
AFTER: table.getSelectedRows() = [1, 2, 3, 4]
rowsToSelect = [0, 2, 4]; Sorter = javax.swing.table.TableRowSorter@3a6727
BEFORE: table.getSelectedRows() = [0, 2, 4]
AFTER: table.getSelectedRows() = []
rowsToSelect = [0]; Sorter = javax.swing.table.TableRowSorter@3a6727
BEFORE: table.getSelectedRows() = [0]
AFTER: table.getSelectedRows() = []
rowsToSelect = [0, 1, 2, 3, 4]; Sorter = javax.swing.table.TableRowSorter@3a6727
BEFORE: table.getSelectedRows() = [0, 1, 2, 3, 4]
AFTER: table.getSelectedRows() = []
rowsToSelect = [3, 4]; Sorter = javax.swing.table.TableRowSorter@3a6727
BEFORE: table.getSelectedRows() = [3, 4]
AFTER: table.getSelectedRows() = []
---------------------------------------------------------

So, in cases when RowSorter = null, new TableRowSorter(model) the selection is not cleared.