Restart altcoin blockchain
You need to delete the data directories entirely with the node software shut down when you do that. If both nodes' data directories have been removed and starting one of them still results in the blockchain being downloaded, that means that there is a node that you are connecting to which did not have its data directory cleared. You can find out what node that is by looking in the debug.log file and seeing the IP address of the node that you are connecting to (or is connecting to you).

Alternatively if you generate a new genesis block, you will not have this problem as whatever blockchain you use with the new genesis block will be different from the original blockchain.