RICHARD: I just thought we should touch base, you and I, after that unfortunate incident last week.
RORY: Grandpa, you already called me about that.
This confirms that Rory’s fight with her grandfather was the previous Friday, and that he did already phone her to apologise, most likely the same evening that it occured. We never get to see the apology so don’t know how it went. It’s not known whether Richard apologised for his treatment of Dean, or just for upsetting Rory, but whatever he said, Rory seems to have accepted it and forgiven him completely (Lorelai’s chat with her would have made that easier).
Richard talks to Rory to make sure everything is alright between them, which she quickly reassures him that it is, with a briskly British military, “Buck up, private” (meaning “Cheer up, soldier”).
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