What has changed?

<fb:repeater id="repeater" row-path="rows" parent-path="." unique-row="id" unique-path="@id">
  <fd:convertor type="long"/>
  <fb:on-bind>
    <fb:value id="rowwidget" path="@rowvalue">
      <fd:convertor type="string"/>
    </fb:value>
  </fb:on-bind>
</fb:repeater>

to

<fb:repeater id="repeater" row-path="rows" parent-path=".">
  <fb:identity>
    <fb:value id="id" path="@id">
      <fd:convertor type="long"/>
    </fb:value>
  </fb:identity>
  <fb:on-bind>
    <fb:value id="rowwidget" path="@rowvalue">
      <fd:convertor type="string"/>
    </fb:value>
  </fb:on-bind>
</fb:repeater>

Can the upgrade be done automatically?

Run the Ant task "Woody2CocoonForms" which is part of the Cocoon build system (run "build Woody2CocoonForms" from your Cocoon base directory). It can also be used to upgrade your custom projects as it requests you to enter the directory which has to be changed at command line.