After mysql_upgrade to 5.7, optimizer not using index on large IN clause
You may not be aware of this, but MySQL optimizer has a different setting between versions

For MySQL 5.6, optimizer_switch looks like this:

mysql&gt; SELECT @@optimizer_switch\G
*************************** 1. row ***************************
@@optimizer_switch: index_merge=on,index_merge_union=on,
                    index_merge_sort_union=on,
                    index_merge_intersection=on,
                    engine_condition_pushdown=on,
                    index_condition_pushdown=on,
                    mrr=on,mrr_cost_based=on,
                    block_nested_loop=on,batched_key_access=off,
                    materialization=on,semijoin=on,loosescan=on,
                    firstmatch=on,
                    subquery_materialization_cost_based=on,
                    use_index_extensions=on


For MySQL 5.7, optimizer_switch looks like this:

mysql&gt; SELECT @@optimizer_switch\G
*************************** 1. row ***************************
@@optimizer_switch: index_merge=on,index_merge_union=on,
                    index_merge_sort_union=on,
                    index_merge_intersection=on,
                    engine_condition_pushdown=on,
                    index_condition_pushdown=on,
                    mrr=on,mrr_cost_based=on,
                    block_nested_loop=on,batched_key_access=off,
                    materialization=on,semijoin=on,loosescan=on,
                    firstmatch=on,duplicateweedout=on,
                    subquery_materialization_cost_based=on,
                    use_index_extensions=on,
                    condition_fanout_filter=on,derived_merge=on


You could set the default for optimizer_switch for MySQL 5.6 in my.cnf and restart MySQL 5.7. Then, the optimizer's behavior will be the same as before the upgrade. For the new options, set duplicateweedout=off and derived_merge=off.

This is not a complete answer. You'll have to test this.