dbmax:
Concerning question 1., if the Examiner has "found" and element or limitation in a reference that you don't think is there and, notwithstanding, still allows the claim, your client is in a good position. I'd go so far as to say golden. Remember the presumption of validity, the clear-and-convincing standard, and deference to the Office's "special expertise".
In my experience, a court ajudicating the validity of a claim will consider Examiner's reasons for Allowance as part, but only as one part, of the prosecution history. But your response, or lack thereof, would likely only come into play if the reasons for allowance included a limiting, not expansive, synopsis of the art vs. the claims. In your particular scenario, as I best understand it, I'd take the money and run.
If there is a bona fide 102 issue, as posited by "JustAnother", you need to remostrate with the client. But keep in mind - as I understand the comment - the reference was before the Examiner during examination. Even if the Office called a "strike" as a "ball", a challenger will bear a "heavy burden" if they wish to invalidate the patent as anticipated by that reference that was before the Examiner.
Concerning question 2, what paragraph of 112 are you referring to? In my experience, the Office routinely allows claim with blatant failure of anteceedent basis. These are a pain to opine on. Shame on the Office for missing these things. The command to not "rewrite claims" just to preserve their validity not withstanding, I don't recall a case in which the CAFC scuttled a claim on this basis.