Magento -- MySQL Heavy CPU Usage Then Fail When Update Product Categories in Bulk

I am running Magento 1.9.3 with 140,000 products on a dedicated server that is still in development mode.

When I try to bulk change categories on products (Catalog -> Manage Categories -> Category Products), I will get an innodb timeout error. When I increase the time to four hours, the job never finishes. When I check the processes, MySQL will work it's way up to using all of the CPU time and then time out. I am able to update the product categories on products individually, but I have about 15,000 to do, so this will not work.

I have tried the following:

Magento Database Repair tool (did not find any errors)
Truncated the log files (This cleared 700MB from the database and improved performance, but does not fix this issue.)
Run mysqlcheck on the database (did not display any errors)
Transferred the SQL database from the server to my personal computer and replicated the error demonstrating it is not a problem with my server. The server is a high end machine with lots of RAM and using an SSD for the database.
Tested the problem on older database backups. If I go back three months, I am able to resolve the issue.

If I restore the three month old backup, I could probably get up to speed on it within a day of work, however the problem is I do not know what caused the issue or whether it will reappear. Since it is causing such high CPU usage on a server that has already been hardware and software optimized for Magento and a large database, I think there is an infinite loop somewhere.

I have a dedicated Magento dev shop looking into this, but it has entirely stopped everything I can do with the site. Can anyone suggest anything before I determine I may have found a bug?

Solution

Solution is that you have to change mode of Index Management from system-> Index Management and change Index Mode to Manual Update from Update on Save and submit. This will help to reduce time while update products in category.