Of course no problem!
Query blocks have a maximum timeout of ten minutes on Cloud. I would think that increasing it to two minutes would be enough but you might just need to add more time 
You might just need to increase the amount of time the block has before the front end "thinks" it should throw an error due to a lack on a response from the backend/DB to confirm that the bulk update has succeeded.
Is the error showing up on the two minute mark or is it occurring sooner? If it happening sooner then we might need to dig around to find out why it isn't waiting until the time limit to error.
Also, here is a useful thread about using looping/chunking to break up a query into smaller parts. This could be useful if you want to scale up the number of objects you are updating or want to break down what you currently have to ensure each batch is succeeding with a smaller load.