VMware support told me to use the built in appstack update process to accomplish this (same as if you were updating an appstack with new software version etc.) They told me it automatically replaces those with the latest version during this process. I haven't tested yet.
It could be me but I have no idea why they keep on saying this, for as far as I know this is NOT true. The moment you update an appstack it does not copy the snapvol.cfg and other files from the new template into this disk, how should it now that as it does not touch the template at all when updateing an appstack.
The only way to update it now is to first upload the new template, then attach that to a machine that does not have an Appvolumes agent, copy the snapvol.cfg and any other changed files from it.
After that select Update from the Appvol Manager and DO NOT start capturing already. Just attach that new disk to the same basic machine without Appvolumes installed, and copy the files from the template onto that disk. Thing is if you do start capturing it will eventually seal the disk as read only and you cannot add files to it anymore.
If there is a nother way, please feel free to add the option how to do it.
That being said, we also have a bunch of different appstack template version. To be honest most of the time there is no need to update the appstacks with the new template files. If you do have an issue with an appstack your better of just recreating that one appstack or change the files in that one appstack. Most of the application you package are not that complicated that it needs a new template.
