Sphinx2.x is upgraded to Sphinx3, and Sphinx3.1.1 is installed on Win7 for testing. The removed data in the delta incremental index cannot be removed from the full index main. It is completely possible in Sphinx2.x.
 Total 2 tables documents (id...) Sphinx (tb,id,type) 
 perform steps: 
indexer.exe -c d:/sphinx3.conf --all -sharp 
searchd.exe -c d:/sphinx3.conf & -sharp 
-sharp documentsid=12id=1sphinx 2("doc",1,0),("doc",12,1) 
-sharp 
indexer.exe -c d:/sphinx3.conf delta --rotate
-sharp 
indexer.exe -c d:/sphinx3.conf --merge main delta --merge-klists --rotate -sharp 
the configuration file sphinx3.conf is as follows
source src1
{
    type            = mysql
    sql_host        = localhost
    sql_user        = root
    sql_pass        = 000000
    sql_db            = test
    sql_port        = 3306
    sql_query        = \
        SELECT id, group_id, UNIX_TIMESTAMP(date_added) AS date_added, title, content \
        FROM documents
    sql_attr_uint        = group_id
    sql_attr_timestamp    = date_added
}
source src1delta : src1 {
    sql_query = \
        SELECT id, group_id, UNIX_TIMESTAMP(date_added) AS date_added, title, content \
        FROM documents WHERE id in (select id FROM sphinx where tb="doc" AND type=1 )
    sql_query_killlist = SELECT id FROM sphinx WHERE tb="doc" AND type=0
    sql_query_post = DELETE FROM sphinx WHERE tb="doc"
}
index main
{
    source    = src1
    path    = d:/sphinx3/data/main
}
index delta {
    source = src1delta
    path = d:/sphinx3/data/delta
    kbatch = main
    kbatch_source = id
}
index rt
{
    type            = rt
    rt_mem_limit    = 128M
    path            = d:/sphinx3/data/rt
    rt_field        = title
    rt_field        = content
    rt_attr_uint    = gid
}
indexer
{
    mem_limit        = 128M
}
searchd
{
    listen            = 9312
    listen            = 9306:mysql41
    log            = d:/sphinx3/log/searchd.log
    query_log        = d:/sphinx3/log/query.log
    read_timeout        = 5
    max_children        = 30
    pid_file        = d:/sphinx3/log/searchd.pid
    seamless_rotate        = 1
    preopen_indexes        = 1
    unlink_old        = 1
    workers            = threads
    binlog_path        = d:/sphinx3/data
}
