Do you need the subjunctive twice?

Hola Alice

Without seeing exactly what you've seen written, in context, it's a bit difficult to answer, but I imagine you may have seen something like this, for example,

- Lo que sea, el caso es que yo no te creo para nada.

This, for example, could be a reaction to someone giving excuses about having done something wrong, and another person reacts saying something like that. This "lo que sea" here would mean "Whatever" as well, but it's more like a set expression, pretty much meaning "I don't care about what you just said".

Another example could be:

- Puedes confiar en mí y pídeme lo que te haga falta, lo que sea. 

Here we are dropping it but you could have also said "sea lo que sea" with the same meaning. So, yes, we do drop it sometimes if what we mean is "whatever it is". 

Saludos

Inma