How would any automated process determine how the link was broken. Was the File deleted or renamed or moved? If the file was deleted the link can not be resolved. If the file was moved how would the automated process find where the file was moved to. Template with smart object layer are normally changed by replacing the Template Smart Object Layer's object with an object that has the same sized and resolution as the template's object so the layer's associated Transform works correctly..
JJMack If the file is deleted or renamed or moved, definitely it doesn't work. That is the reason I have defined the generic template. You much have to use that template with the same folder structure and same bottle name. I am brainstorming If I can do this with photoshop scripting.
Why do you need smart object layers in you template in the first place? If you change a bottle it will only change you template when you open the template in Photoshop. No Populated template will be updated that were saved as flat files, Any populated Templated saved as a PSD file will only be updated it they are opened in Photoshop. If you do not delete, rename or move your files used in your templates you should not have a Problem with Broken Links. Photoshop is programmed to allow you to resolve broken links when you open a template with a broken link so the process is automated as best it can be. You the one that would know what happened to the linked file. Smart Objects are not cataloged and maintained in a library system. Photoshop would have no idea what happened the linked file other then its not there.