Estonia taxes the margin, not the price. Put in what you paid and what you sold it for, and you get the VAT under the margin scheme.
Secondhand goods are not VAT-free. If you are registered, the scheme changes what is taxed, from the price to the margin. It does not change whether you owe.
A margin-scheme invoice shows no VAT amount. It carries the note required by KMS §37(8)(7) instead.
A loss on one item does not reduce the VAT on the next one. Netting a whole period together is a separate method, and the tax authority has to approve it in writing first.
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This is an estimate, not tax advice. The margin scheme is EU law, and each country writes it into its own rules differently. Check with the tax authority or your accountant before you file anything.