According to the Sequelize documentation, it looks like the where clause and the transaction should be in the same object.
Could you replace:
await myCovers.update({ refunded: amount }, { where: { id } }, { transaction });
// update number 2
await myCovers.update({ refunded: amount }, { where: { id2 } }, { transaction });
by
await myCovers.update({ refunded: amount }, { where: { id }, transaction });
// update number 2
await myCovers.update({ refunded: amount }, { where: { id2 }, transaction });
Tell me if it helps