MySQL InnoDB stop locking when large sql is executed

Question

We face a issue that the InnoDB table is locked, when a sql file that is executed is large than a certain file size.

The problem does not appear when the file size is much lower, for example 25MB. But when the file increase to something like 45+ MB the InnoDB table locks, when the sql is on 70% of running.

Is this something that we can prevent by changing our my.cnf or something else?

Our current my.cnf:

[mysqld]
sql_mode=""

bind-address = 127.0.0.1
local-infile=1
innodb_file_per_table=1
innodb_file_format=barracuda

skip-name-resolve
performance_schema=ON

slow_query_log = 1
slow_query_log_file=/var/log/mysql-log-slow-queries.log

# key_buffer_size = 390M
max_allowed_packet = 200M
# sort_buffer_size = 16M
# read_buffer_size = 16M
read_rnd_buffer_size = 2M
# myisam_sort_buffer_size = 64M
tmp_table_size = 300M
query_cache_type = 1
query_cache_size = 650M
query_cache_limit = 2M
query_cache_min_res_unit=512
thread_cache_size = 100
max_connections = 225
wait_timeout = 900
connect_timeout = 120
innodb_buffer_pool_size = 8G
max_heap_table_size =290M
innodb_log_buffer_size = 36M
# join_buffer_size = 32M
innodb_buffer_pool_instances = 8

long_query_time = 5
table_definition_cache = 4K
open_files_limit = 60K
table_open_cache = 50767
innodb_log_file_size= 256M
innodb_lock_wait_timeout = 1000
innodb_lru_scan_depth = 100
innodb_flush_neighbors = 0
innodb_io_capacity_max = 10000
innodb_io_capacity = 5000

innodb_purge_threads = 4
innodb_flushing_avg_loops = 10

Small part of the sql file:

SET NAMES 'utf8';
SET CHARACTER SET utf8;
/************** SYSTEM ******************/
UPDATE `catalog_product_entity` SET  `updated_at` = '2018-09-24 08:45:15',  `updated_by` = '23'   WHERE `entity_id` = '158700';
UPDATE `catalog_product_entity` SET  `updated_at` = '2018-09-24 08:45:15',  `updated_by` = '23'   WHERE `entity_id` = '158701';