This issue was resolved in a separate thread, but I'm pasting the info here to close the loop.
The other cache you mention is located at ~/.appscale/locations-<your-keyname>.json
on the machine you are using the tools on. The file was created for
cloud deployments in order to keep track of IP addresses in a cloud
deployment that aren't listed in the AppScalefile. It definitely needs
some work in order to handle situations like the one you described.
You
can also perform a "down" without using the tools by running the
AppController/terminate.rb script on all the machines in the deployment.
For a "down --clean", you would run `ruby /root/appscale/AppController/terminate.rb clean`. Just keep in mind that a clean will remove all application data, user data, and logs.
For this use case, I
would recommend doing an `appscale down` before stopping the machine
the first time. After restarting the machine with a new IP address,
remove the ~/.appscale/locations-<keyname>.json file, modify
the AppScalefile with the new IP address, and do an `appscale up`. The
app should get automatically deployed, and it should retain all of its
data.