Hello,
Advanced Installer can't seem to copy a subdirectory structure
Advanced Installer cannot copy empty directory structures but there might be a workaround if this is what you mean. If not, can you please give us more details about the subdirectory structure?
Is there a way for AI to ignore a previous installed program with the same name and version and install anyways?
You can try to do this by creating a template of the project with the same version and name. This way, it will have completely new component GUIDs and also the Product Code changed.
As a generic note, although the package needs to be customized according to the user machine there are some changes that need to be done at build time as well as at install time. In this case I recommend you perhaps consider integrating an automatic build as part of the deployment process.
All the best,
Mihai