Are the change values submitted to the server before or at the moment of generating the PDF.
When using a dynamic action of the type "Set value" only the value on the cliënt side is set. And the generation of the PDF uses the value of the page item in session state.
What you could do is turning the "Set value" actions to execute PL/SQL code in which you set the page items using bind variable notation. And return the value to also set it cliënt side.
If the page items are only rendered on the page for debug purpose I would only set the page items on the server side. Use the session link in the developer toolbar to see if the value has changed. Don't forget to refresh the session popup every time the dynamic action has run. And I would set the condition of these items to never so they are never generated on the page.
If you're on apex 4.2 you can set multiple page items with different values using only one "Set value" dynamic action.