How do I fix this? I've already tried
truffle migrate --reset and/or deleting the .json files.
This is a message from truffle framework saying that you are trying to call a function from an address which is not a contract. This is no a solidity error message.
Since you are writing about calling selfdestruct function on your contract I can only assume that you have killed your contract and then tried to call its function using truffle framework.. For example during test.
So the scenario is that you kill your contract and then try to call some of it's function. Then you will get such an error message.