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 RotS, 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 R2D2 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 answert to Was Yoda fully sane on Dagobah?