My question is if I omit the new key setting for updates that do not requirethe .msi to be replaced will it delete the key or leave it unchanged?
wyBuild doesn't compare the registry changes (it's too complex a problem). So it takes the registry changes of the latest version as literal.
So if you omit a key that was in a previous update, then when wyUpdate installs the new version it will leave the registry key/value completely untouched.
Does that make sense?