Hello Lacepeb -
Apologies for the delayed response.
Yes, if you select a different template for a listing, the initially selected template will no longer be applied. So, if you have a custom template that you are using selecting from any of our available templates would replace that template on to whichever listing you are working on.
If you are running into trouble with a custom template, please feel free to let us know the details of what you are running into in a support case and we'll be happy to assist you.