Dan,
First, I would filter the main ministers list to find all Subsitute EMHCs.
Next, select them all (or the appropriate portion of them) and assign them to the Head EMHC and/or Regular EMHC subdivision(s) of the EMHC ministry. Don't forget to click the substitute checkbox. Depending on each minister's qualifications, you might need to select a single minister multiple times to completely and correctly assign all substitute ministers.
Finally, select all Substitute EMHCs again and remove them from the Substitute EMHC ministry before deleting that ministry from your list of ministries.
Jennie