I've tried both CheckAdd and CheckMod, and have been unable to set the RefNumber using QuickBooks Pro 2012 on Windows XP. I searched for RefNumber in the QuickBooks SDK Concepts Manual and didn't see anything that might address this problem. On the web, I did see a QODBC post on the topic.
Here's the CheckMod I tried. I don't receive an error when I issue this request; the RefNumber just isn't set.
<?xml version="1.0" encoding="utf-8"?>
<?qbxml version="11.0"?>
<QBXML>
<QBXMLMsgsRq onError="stopOnError">
<CheckModRq>
<CheckMod> <!-- required -->
<TxnID >85-1388374219</TxnID> <!-- required -->
<EditSequence >1388374219</EditSequence> <!-- required -->
<RefNumber>12345678901</RefNumber>
</CheckMod>
</CheckModRq>
</QBXMLMsgsRq>
</QBXML>