Are empty crates charged with VAT on return transport to the EU?

If you import goods from a non-EU country, you pay VAT. This rule also applies to the return transport of empty crates. If you not want to do this at Customs you can also account for it in your VAT return? This way you pay nothing on balance and you prevent unnecessary confiscation of your liquidity. You can read more about applying for a permit here.
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