Hi Darielmarlow,
Thanks for posting here.
It will not provision new machine, If you are manually making changes by remoting into the VM, then if due to unknown reason the VM is re-provisioned (for ex: service healing, maintenance etc) then the changes you have made will be lost.
The recommended way to update your deployments/applications is to upload the .cspkg and .cscfg manually from the classic portal or using visual studio.
Ref:
https://azure.microsoft.com/en-in/documentation/articles/cloud-services-how-to-manage/
Hope this helps.
Girish Prajwal