AS3 Pool and Members

Is your automation tool using AS3 to add the pool members? In any manner, if you post the AS3 declaration with no pool members, then it will indeed delete those pool members. Ideally, you would deploy in the same manner you use today, update your automation tool to use AS3 to add/remove pool members, then query the current configuration and make changes to the current configuration for future AS3 declarations. 

If your automation tool cannot take advantage of AS3, you should then consider those configurations as untouchable with AS3 post-deployment. Otherwise you'd need a programmatic way to query the current AS3 declaration, query the pool members using iControlREST, and have those members added to the declaration. That would not be easy or the best way forward.