Is there a specific proof in the canon (of any kind) showing that R2-D2 had met/seen/been aware of existence of Master Yoda at any time between the siege of Naboo and Yoda going into Exile on Dagobah?
The most plausible possibility I can think of is on Senator Organa's ship at the end of Revenge of the Sith, right before they split the Skywalker twins. But I don't remember if it was explicitly shown that R2 was in a position to see Yoda (as opposed to, say, being in the engineering areas of the ship).
NOTE: This question is very closely related to this one: Why does R2-D2 try to electrocute Yoda? - but that question's answers seem to have merely glossed over whether R2-D2 saw Yoda before.
That said, I'm going to continue my answer with the assumption that R2 HAS seen Yoda, but I have no evidence for this. (from Jeff's winning answer)
This question itself was prompted by Chad's comment to my answer to Was Yoda fully sane on Dagobah?