IBatchItems

using System.Collections.Generic;

IBatchItems batch = Batch.AsBatchItem.ChildItems;
List<string> docDefs = new List<string> {"DocSet","Doc1","Doc2"}; // Document assembly order
          // Key field name
          // (the field should be indexed in all documents and have the same name)
string keyFieldName = "SSN"; 
List<string> keyFields = new List<string>();

// Disassembling sets
bool foundChildren = false;
do
{
    foreach (IBatchItem itm in batch)
    {
        if (itm.ChildItems.Count > 1)
        {
            int shift = 0;
            foreach (IBatchItem subItm in itm.ChildItems)
            {
                shift++;
                batch.Move(subItm, itm.Index + shift);
            }
        }
    }
    foreach (IBatchItem itm in batch)
        if (itm.ChildItems.Count > 1)
            foundChildren = true;
} while (foundChildren);

// Sorting documents the way they should be in the set
          // (i.e. the set itself followed by all its subdocuments)
foreach (string docDefName in docDefs)
{
    List<int> indexList = new List<int>();
    foreach (IBatchItem itm in batch)
        if (itm.Type == TBatchItemType.BIT_Document)
            if (itm.AsDocument.DefinitionName == docDefName) indexList.Add(itm.Index);
    for (int i = 0; i < indexList.Count; i++)
        batch.Move(batch[indexList[i]-i], batch.Count);
}

// Searching for all options of key fields in the batch
foreach (IBatchItem itm in batch)
{
    if (itm.Type == TBatchItemType.BIT_Document)
    {
        string keyFieldValue = (string)itm.AsDocument.IndexedItemValue(keyFieldName);
        if (!keyFields.Contains(keyFieldValue))
            keyFields.Add(keyFieldValue);
    }
}
// Assembling documents with the same key field
foreach (string keyFieldValue in keyFields)
{
    List<int> indexList = new List<int>();
    foreach (IBatchItem itm in batch)
         if (itm.Type == TBatchItemType.BIT_Document)
            if ((string)itm.AsDocument.IndexedItemValue(keyFieldName) == keyFieldValue) indexList.Add(itm.Index);
    for (int i = 0; i < indexList.Count; i++)
        batch.Move(batch[indexList[i]-i], batch.Count);
}

// Moving subdocuments into sets only if key fields match
// (set sections first, child documents second)
int ind = 0;
while (ind < batch.Count)
{
    if (batch[ind].Type == TBatchItemType.BIT_Document)
        // Looking for the beginning of the set
        if (batch[ind].AsDocument.DefinitionName == docDefs[0])
            // If a document after the set is not a set and key fields match,
            // we add it to this set
            while (ind+1 < batch.Count && 
            batch[ind+1].AsDocument.DefinitionName != docDefs[0] && 
            (string)batch[ind+1].AsDocument.IndexedItemValue(keyFieldName) == (string)batch[ind].AsDocument.IndexedItemValue(keyFieldName))
                batch[ind].ChildItems.Move(batch[ind+1], batch[ind].ChildItems.Count);
    ind++;
}