mysql occupies 300 gb tmp folder space. i think its dirty pages flushing

**I have two innodb tables which has about 15 million records and 1.8 Million records respectively. I have tried all possible settings and everything is only worsening the problem. Earlier it use to create tmp files which occupies only 70 GB file. But today it is still running and it occupies about 350 GB and its running for last 6 hours. This happened only after I changed innodb_flush_log_at_trx_commit = 0 (earlier it was 2) and innodb_max_dirty_pages_pct = 10 (ealier it as 75)My site is not coming regular intervals. In my old setting it use to run everyday and occupied 70 gb and now its running every week. Yesterday we updated around 90000 records in the table. I am not getting any solution for this innodb issue. my.cnf setting is below
innodb_flush_log_at_trx_commit = 0

innodb_log_buffer_size = 4096M
innodb_io_capacity=5000
innodb_adaptive_hash_index = ON
innodb_max_dirty_pages_pct = 10
innodb_adaptive_flushing = false
query_cache_limit = 32M #16M #1M
query-cache-size = 2GB #1GB
query-cache-type = 0
myisam_sort_buffer_size = 48GB #16GB
bulk_insert_buffer_size = 1024M #512M #32M
innodb_log_file_size = 1GB #512M
thread_concurrency = 512 #256 #16
open_files_limit = 65535 #9786432
join_buffer_size = 262144
table_definition_cache = 1024M #512M #6M
table_open_cache = 1024M #512M #4M
table_cache = 1024M #512M #4M
max_connect_errors = 12000
interactive_timeout = 1100 #down from 28800
wait_timeout = 1100 #down from 28800
max_heap_table_size = 120M #32M
tmp_table_size = 120M #32M
max_connections = 1000
read_rnd_buffer_size = 32M #16M #1536K
read_buffer_size = 32M #16M #1536K
sort_buffer_size = 32M #16M #2M
thread_cache_size = 8192 #4096 #2048
thread_stack = 1M #512K 256K
max_allowed_packet = 1024M #512M 16M
key_buffer = 8G #4G
slow-query-log-file=/var/log/mysql/mysql-slow-queries.log
long_query_time = 4
innodb_buffer_pool_size=13GB #1GB
innodb_file_per_table=1
symbolic-links=0
tmpdir=/backup-data/mysql-tmp
user=mysql

contents of tmp folder

This is the tmp folder contents
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Dirty pages don’t get flushed into the temp directory. Those are temporary tables from queries. You have a problem with bad execution plans.

yes actually i found this after running show process list. I had to kill the queries manually. We are using he same query for long time. I use the same query after killing it, it worked fine. Do you have any idea why this happenned?