Unlike academia, the movie industry doesn't appear to have any definitive "rules" or "best practices" in place to handle this type of situation; I expect that the Wachowski sisters are going to be largely defining how this works based on how the industry handles it and how they react.
However, there does seem to be a trend emerging that it's still acceptable to refer to their work that was done before transitioning as being done by "The Wachowski Brothers". As one example, Wikipedia still says:
The Matrix is a 1999 American-Australian neo-noir science fiction action film written and directed by The Wachowski Brothers
The consensus over there seems to be that the credits on the film name them as the Wachowski Brothers (several attempts to "fix" the article have been reverted), so it's still correct to identify the people who directed that movie, at that time, by that name. (I believe this is what would happen if, for example, a director legally changed their name, or chose to use a pseudonym, or any other event that would make their current legal name different from the credits.)
On the other hand, when discussing the sisters themselves, it's more correct to use their current gender identities, even when the topic includes things they did previously. For example, the 2015 book Gender, Race and American Science Fiction, when discussing their Matrix work (it was written before Lana transitioned), says:
While the Wachowski siblings did conceive of the Matrix story as a trilogy...
Of course, many sources just avoid the whole issue by referring to the siblings as "The Wachowskis". The Wachoskis themselves seem to be pretty laid back about the whole situation. At the premier of Cloud Atlas, Andy Wachowski introduced the sisters as "Wachowski Starship".src