[n0mad01]

I'm also using Beanstalk for a (big) PHP application, it was a bit of a mess rewriting all data saving to S3, email via SES, routing with Route 53 and such stuff.

Beanstalk is not 100% matured, you see this in some unexpected behaviors like :

- changing some environment vars give unexpected troubles with the load balancers in one environment, but not in another. - restarting an app server sometimes crashes the environment. -etc.

the automatic procedure is that beanstalk starts replacing it's EC2 instances from your Auto Scaling Group, which sometimes has to be repeated for 2-3 times in a row which can take up to 30 mins.

in the meantime you should switch to a backup environment ( which is a must have! )

but all in all im positive because it's getting better all the time and the benefits are despite the disandvantages great.

check out the beanstalk forum : https://forums.aws.amazon.com/forum.jspa?forumID=86