2. Do we mount the VMDK for the app stack onto a none App volumes machine and amend the file?
No you can't because the appstack is read only, you cannot edit it after sealing the appstack
3. Does App Volumes manager have a magic button that will replace all app stacks with the new template files if we amended the template VMDK file?
No it doesn't. It does have an option to change a writable during login. If you are using writables and need to change that you cloud do it trough the manager.
1. Do we go into app volumes manager and click update on every one of them and update this way?
So that leaves option 1. Yes, you need to click update and edit the appstack then. I would suggest attaching the updated appstack (before sealing) to a machine that does not have an Appvolumes agent installed and change the snapvol.cfg. After that attach it to the packaging machine and seal it right away.
Also make sure to edit the template, this is read/write so just attach it to a machine without Appvolumes manager and edit the snapvol.cfg.
Do you use writable volumes in your environment?
If so, you can use the update feature in the writable volume section, update the snapvol.cfg there and then you don't have to update the individual app stacks.