I had forgot about this little document while at a client site, so here it is for reference:

If you have already developed BizTalk Server artifacts that use the native MLLP adapter you must delete and recreate them with the updated MLLP adapter.
To update the existing MLLP adapter
1.               Using Windows Explorer create the C:\MLLPTemp\ folder.
2.               Click Start, point to Programs, point to Microsoft Visual Studio .NET 2003, and then click Microsoft Visual Studio .NET 2003.
3.               In Microsoft Visual Studio .NET 2003, click View on the toolbar, and then click BizTalk Explorer.
4.               In BizTalk Explorer, expand erver name>.BizTalkMgmtDb.dbo, expand TwoWayAckReceivePort, expand Receive Locations, and then right-click TwoWayAckReceiveLocation, and the click Edit.
5.               In the Receive Location Properties - Configuration - General dialog box, in the Transport Type drop-down box select File.
6.               In the Receive Location Properties - Configuration - General dialog box, in the Address (URI) box click the ellipsis (…) button.
7.               In the File Transport Properties dialog box, in the Receive folder box, type C:\MLLPTemp\.
8.               Click OK.
9.               In the Receive Location Properties - Configuration - General dialog box, in the Receive Handler drop-down box select BizTalkServerApplication.
10.           Click OK.
Note  If you have any BizTalk Server artifacts configured using MLLP adapter, you must repeat steps 3-9 for each artifact before proceeding. Be sure to save the configuration information so that you can update the artifacts using the updated MLLP adapter. You must also save Receive and Send Handlers configuration information if you have customized the MLLP adapter.
11.           Click Start, point to Programs, point to Microsoft BizTalk 2004, and then click BizTalk Server Administration.
12.           In the BizTalk Administration Console, expand Microsoft BizTalk Server 2004 (Local), expand Adapters, right-click the MLLP from the list, and then click Delete.
13.           In the BizTalk Server Administration dialog box click Yes.
14.           In the BizTalk Administration Console, right-click Adapters, point to New, and then click Adapter.
15.           In the Add Adapter dialog box, in the Name box type MLLP, in the Adapter drop-down select MLLP, and then click OK.
16.           Close the BizTalk Administration Console.
17.           In Microsoft Visual Studio .NET 2003, in the BizTalk Explorer, click Refresh on the toolbar.
18.           In the BizTalk Explorer, right-click TwoWayAckReceiveLocation, and the click Edit.
19.           In the Receive Location Properties - Configuration - General dialog box, in the Transport Type drop-down box select MLLP.
20.           In the Receive Location Properties - Configuration - General dialog box, in the Address (URI) box click the ellipsis (…) button.
21.           In the MLLP Transport Properties dialog box, do the following:

22.           Click OK.
23.           In the Receive Location Properties - Configuration - General dialog box, click OK.