If you want to change the genesis block, then you'll be changing the block hash. With this you'll render the rest of the blockchain invalid.
UPDATE: However there are field in the genesis block that do not contribute to the block hash and thus would not require the following
A new genesis block will require a new chain being built. On MacOS, the get init <path to genesis> command locks the /Users/[user]/Library/Ethereum/geth/chaindata folder by default. This would be shared by different nodes if you didn't explicitly specify a different datadir.
What is the datadir? - It's a data directory for the databases and keystore associated with a node, in other words, a location where to create the blockchain.
Example:
geth --datadir <path_of_data_directory> init <path_of_genesis_file>
An example value of the <path_of_data_directory> could be Library/Ethereum/aCoolDataDirectoryName. Then within that directory you'll have the following:

By specifying a different datadir, you'll be able to keep your old blockchain but create a new one with your new config.
Sources:
Command Line Options
Related Question