If a ship has command tokens equal to its Command value and it gains another command token (through whatever means) is that new token discarded or can an existing token be replaced by the new token?

You choose which token is discarded, as per the rulebook

RRG, Page 3, "Command Tokens"

• When a ship is assigned a command token, if it has more command tokens than its command value, it must immediately discard one of its command tokens.

Assign the new Command. Have Excess tokens to value. Discard one of the tokens. Does not have to be the new one, its your choice as to which one.

Awesome. Thanks.