Steps to reproduce:

1. Database clustered in multi master mode with 200GB of data
2. Upgrade from 5.0.14 to 6.0.7

Result:
The first part is working well but at one point, there are queries taking 14 000 seconds each.

select distinct i2.key_ from items i join item_discovery id on id.itemid=i.itemid join items i2 on id.parent_itemid=i2.itemid join functions f on i.itemid=f.itemid and f.triggerid=13272 where i.flags=2

After 2 days, the queries are not done.

I attach the describe and explain queries. I will put later the explain one as it takes a long time.

Let me know if you need more information 

Regards,
Nathan