Funds are missing from your Nintendo eShop balance on Nintendo Switch.
If this relates to the Nintendo eShop for Wii U or Nintendo 3DS please refer to End of Purchases in Nintendo eShop for Wii U and Nintendo 3DS.
Verify whether the purchase was made on a different console.
Verify which Nintendo Account the funds were added to.
Funds are not transferrable and are not shared between different Nintendo Accounts.
Funds added to one Nintendo Account will only be available when signed in with that Nintendo Account.
If you have more than one Nintendo Account linked to your console, check the balance for each Nintendo Account to see if the funds were added to a different Nintendo Account than the one you were using.
Make sure the funds were added for the same country/region that your Nintendo Account is set to.
Your Nintendo eShop account balance does not carry over if you change your Nintendo Account country/region setting.
If you have added funds while the Nintendo Account is set to one country/region, you will need to use the remaining funds before you can change the country/region setting.