I have to agree with Shinji, we too had all templates set up and new app has wiped these out. Trying all morning to get the invoices looking slightly like they did, but for some reason (whether this is a bug or not) using the same liquid and html coding as before creates an entirely different look.
Some prior notice would have been appreciated so that we could have prepared, instead of finding these changes just as we're about to print of a whole load of orders. We now have to delay order packing, while we work on sorting this mess out.
Love Shopify and it's fantastic new changes and I am in no doubt that this new app will be great, however please offer some warning as this has completely thrown us off.