At the very end of Star Wars Episode 1: The Phantom Menace movie, Mace Windu and Yoda had this conversation:
Mace Windu: There is no doubt. The mysterious warrior was a Sith.
Yoda: Always two there are....no more...no less. A master and an apprentice.
From this conversation, it's clear that they had no idea about the other Sith (They were surprised to see one Sith). They were just using their knowledge of Rule of Two to guess that one other must be alive.
In Star Wars Episode 3: Revenge of the Sith, Yoda told Palpatine Darth Sidious. I thought, Yoda discovered Palpatine's Sith name from security hologram.
But, in the last episode of Star Wars: The Clone Wars - The Lost Missions (Unfinished season 6), Yoda called Darth Sidious by his name.
How does Yoda know the name of Darth Sidious? Has Yoda encountered Darth Sidious after the events of TPM?