It might happen that an exchange announces to delist a coin. You should check coinmarketcap.com, if there is another exchange and transfer them there. If there is no other exchange available you might have to enter them as "[OUT] Lost" if it is compliant with your local tax regulations.
You can record the coins as lost using the manual entry on the "Transactions" page. Click New button and select "[OUT] Lost" as the Transaction type. After that please enter the amount and currency of the coin.
The LOST transactions are listed in the "Lost and Stolen Report" as part of your tax report.
You can also use the lost or stolen transaction type if the coins have been stolen, e.g. through a hack.
If there was an automatic conversion to another coin and a withdrawal (delisted coin) and deposit (converted coin) was imported, please change one transaction into a trade and delete the other transaction. If necessary, then work with the start date in the API job afterwards to prevent a re-import of the deleted transaction: How to Set a Start Date