Are you just trying to update the template that is used for newly built full clones without touching the existing? If so you can just just edit the pool and update the template. I would recommend building a test pool and verifying this works as expected in your environment. If you aren't already I would look into backing up your full clones since they sound to be highly customized.
For full clones if you need to upgrade the software/guest OS the entire VM is deleted and recreated so everything would be lost unless you use a profile management tool. I would recommend looking into VMware's User Environment Manager (UEM), Liquidware ProfileUnity or Microsoft's User Experience Virtualization (UE-V) which can capture the profile and configuration data. Using one of these would give you the flexibility to move to Instant clones.