I don't know about the error message you mentioned, that sounds a bit weird. However, disregarding that, the calculator is actually saved with the configuration when you do "update" and then "nlsave". You will however not see it, the calculator is not a separate object, it's attached to the calculator itself. This is the fact which allows you to compute quantities (like transmission spectrum, etc) from the configuration as restored from the NC file without rerunning the self-consistent calculation.
I think we should later make it a bit more obvious that a configuration has a calculator attached to it, but you can see it by dropping the configuration on the Scripter, then it will expand the calculator for you, or rather the parameters defined for the calculator.