Not all issues that arise in patent prosecution are appropriate for appeal. The BPAI has a very specific jurisdiction: claim rejections. That leaves a large number of issues that are outside of the BPAI's jurisdiction, which means you must petition rather than appeal. A long list of these can be found in Chapter 1000 of the MPEP, including:
- Restriction requirement
- Objections to the drawings
- Objections to the specification
- Objections to the claims
- Refusal to enter claims after final
- Refusal to enter evidence after final
- Finality of Office Action
- Refusal to enter appeal or reply brief
- Formal sufficiency and propriety of declarations
- Refusal to give priority date for failure to satisfy conditions in 35 USC 119 or 120
Bringing up these issues in an appeal brief is not damaging per se. The Board will simply refuse to decide on the issue. The damage occurs in cases where waiting until after appeal to resolve the issue is too late.
Not all issues need to be resolved. Maybe you don't think it was proper for the Examiner to make the Office Action final – but you can usually live without a ruling to that effect. Maybe you think the Examiner's objection to the specification for a purported misspelling is improper – the spec really should use the word "discrete" rather than "discreet" – but I'll bet you'd be willing to amend the spec if you win on appeal. (The misspelling objection is, sadly, a true story.)
Some issues can be resolved after appeal, but doing so will cost a great deal of time and money. Suppose your chances of winning on appeal are low unless your declaration evidence is entered. If you think the Board will rule on this in your favor and consider your evidence, you're wrong, and your misunderstanding may result in the Examiner's rejection being affirmed. You can reeopen prosecution after losing on appeal, and enter the evidence then – but this is obviously a big waste of the client's time and money. So if you really want that evidence entered, and you have good facts, you should petition simultaneously with the appeal.
Finally, if you really need a petition to be decided in your favor to get allowable claims, waiting until after appeal can be fatal. That's because almost all the petitions discussed in this post are petitions under 37 C.R.F. § 1.181, which says that petitions "not filed within two months of the mailing date of the action or notice from which relief is requested may be dismissed as untimely." Given that the appeal process takes on the order of years, not months, it's safe to say that the appeal will not be decided within two months of the Office Action that you're petitioning. While it's possible that the petition decision-maker will have mercy and not dismiss as untimely, clearly you don't want to depend on that.
The petition you need a favorable decision will most likely be related to new matter. Imagine winning on substantive issues at the Board, then having a new matter issue blocking you from a Notice of Allowance. Maybe you can deal with the new matter issue by withdrawing the spec amendment that's causing the problem -- only to get a "no antecedent basis in the spec" objection in the next Office Action. Maybe you can deal with the new matter issue by withdrawing the drawing amendment that's causing the problem – only to have the Examiner reinstate the "every feature of the claims must be illustrating in the drawings" objection that prompted your drawing amendment. Therefore, you really should petition the objection as soon as possible.
There is an exception to that: a new matter objection to the spec or drawings that is actually related to the claims should be accompanied by a claim rejection under § 112 First. The new matter objection then becomes an appealable matter rather than a petitionable one. MPEP 608.04(c). In such cases, I think it's best to address this in the Appeal Brief, asking the Board to consider the issue on appeal. Then you can get a decision disposing of both the § 112 rejection and the new matter objections. Though I would probably file a timely petition and pursue the issue on appeal, in case the Board didn't see it as an appealable issue.
For more on the interplay between spec objections and 112 rejections, see my post here and the Board's decision in Ex parte Popp.
I'll be blogging about petitions from time to time. Petitions aren't searchable like BPAI decisions, so it's not as easy to research petition issues. But I read a lot of file histories in my blog research, and sometimes I do come across interesting issues related to petitions, which may lead to a blog post.