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Rebuilding on a new store, or replacing a store you closed? The theme moves as a ZIP, the licence moves from the dashboard, and the two are separate jobs. Most problems come from doing only one of them.
Keep the exported ZIP. It is the only copy of your page layouts. If product templates go missing on the new store, that file is what restores them, and support cannot recover them without it.

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The order that works

1

Export the old theme

In the old store, Online Store → Themes → ⋯ → Download theme file. Shopify emails you the ZIP. Save it somewhere permanent before you touch anything else.
2

Upload it to the new store

In the new store, Online Store → Themes → Import theme → Upload ZIP file. It arrives unpublished.
3

Move the licence

The key is still bound to the old store, so the new one will refuse it. Go to app.ecomelixir.com/licenses, open Actions → Change Store on that licence, and enter the new store’s default .myshopify.com URL. The transfer is immediate. See Transfer a license.
4

Enter the key on the new store

Theme editor, Theme settings → License, paste, save. See Activate your license.
5

Check your product template before publishing

This is the step people skip. See below.
You do not need access to the old store for the licence transfer, and a store you have already deleted is fine. Export the theme before deleting a store, though, because you cannot get the ZIP afterwards.

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”This license is already bound to another shop”

Expected. A licence is active on one store at a time, and uploading the theme somewhere else does not move it. Submit the change of store request described above and the message clears. It does not mean you need a second licence. You only need another licence if you intend to run both stores at once.

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Your product pages are missing

The most common casualty of a store move. Symptoms:
  • The theme editor’s template dropdown shows no templates for products
  • Product pages return 404 on the new store
  • You cannot open a product page to edit it at all
The theme arrived without templates/product.json, so there is no product template for Shopify to render or for the editor to open.
1

Open the exported ZIP

Unzip it on your computer and find templates/product.json. Open it in a text editor and copy everything.
2

Create the file in the new theme

In the new store, Online Store → Themes → ⋯ → Edit code. Under Templates, choose Add a new template, pick product, and select JSON.
3

Paste and save

Replace the contents with what you copied, then save.
4

Repeat for any other missing template

Check templates/ in the ZIP against the new theme. Custom product templates such as product.bundle.json are separate files and each needs the same treatment.
Without the ZIP, your layouts cannot be recovered. Support can install a generic product template so the page renders and you can edit again, but it will not be the page you built.

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What does not come across

Bundles built in a third-party app are the usual surprise. A Kaching or Rapi bundle lives in that app, not in the theme, so it has to be rebuilt on the new store or migrated using whatever that app provides. Ask the app’s support, not theme support. Products and media belong to the store, not the theme. Move those with Shopify’s own export and import, or a migration app, before you judge the theme as broken.

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Troubleshooting

templates/product.json did not make it across. Restore it from the exported ZIP using the steps above.
Same cause. Shopify has nothing to render the product with. Restore the product template, then reload.
Hard refresh the storefront first, since the theme caches the last check in your browser. Then confirm the Licenses page lists the new .myshopify.com URL and that the key in Theme settings → License has no trailing space.
A template JSON is missing or came from a different theme version. Compare templates/ in the ZIP against the new theme and copy across what differs. See Updating manually for handling the save errors that can appear.
Upload the theme ZIP itself, not a folder you zipped yourself and not an “unzip-me” wrapper. Shopify expects the file exactly as it was emailed to you.
Raise a ticket with your licence key and the new store URL. Support can move the licence and put a working product template in place, but your original page layouts are gone and will need rebuilding.

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If it is still not resolved

Raise a ticket with:
  • The old and new .myshopify.com URLs
  • Your licence key
  • The exported ZIP, which support will ask for
  • Which templates are missing