I'am not clear do you want to change hosting place ("site") or template.
If you are changing hosting place then you will need to copy database first,
then copy files and then alter database settings for connection string if needed(configuration.php).
If you are changing template , since module positions are defined in template if new template does not have module position with same name module will not be shown. Noting is lost , only not visible if new template does't have module position with same name.
I didn't know since the release of JV1.6, if anyone has seen some bugs or issues that might have popped up.
How about creating a template based on the virtual home layout. Maybe allowing a user to input a picture with hot spots. I know that the hot spots on (.gif, .jpf, etc) would require an appropriate component, but something like that can be useful.
I am working on a customer (realtor) who want to incorporate a more enticing website experience.