In a nutshell, the default termination policy during scale in is designed to remove instances that use the oldest launch configuration.
Currently, Amazon EC2 Auto Scaling supports the following termination policie:
OldestInstance Terminate the oldest instance in the group. This option is useful when you're upgrading the instances in the Auto Scaling group to a new EC2 instance type. You can gradually replace instances of the old type with instances of the new type.
NewestInstance Terminate the newest instance in the group. This policy is useful when you're testing a new launch configuration but don't want to keep it in production.
OldestLaunchConfiguration Terminate instances that have the oldest launch configuration. This policy is useful when you're updating a group and phasing out the instances from a previous configuration.
ClosestToNextInstanceHour Terminate instances that are closest to the next billing hour. This policy helps you maximize the use of your instances and manage your Amazon EC2 usage costs.
Default Terminate instances according to the default termination policy. This policy is useful when you have more than one scaling policy for the group.
One of the possible solutions could be to use Instance protection. The auto-scaling provides an instance protection to control whether instance can be terminated when scaling-in.
Therefore, enable the instance protection for ASG to protect instances from scaling-in by default. Once you are done with you server, decrease a value of desired number of instances, remove instance protection from particular instance (either using CLI or SDK; note that this protection remains enabled for the rest of instances) and auto-scaling will terminate that exact instance.
For more information about instance protection, see Instance Protection