According to rule 15a:
(1) Amending as a Matter of Course. A party may amend its pleading once as a matter of course within:
(A) 21 days after serving it, or
(B) if the pleading is one to which a responsive pleading is required, 21 days after service of a responsive pleading or 21 days after service of a motion under Rule 12(b), (e), or (f), whichever is earlier.
(2) Other Amendments. In all other cases, a party may amend its pleading only with the opposing party's written consent or the court's leave. The court should freely give leave when justice so requires.
If you are still within 21 days of when you served your original pleading (or their response, if one was required) then you should still be able to amend your pleading.
If you are outside that window, you may be able to use rule 12(c):
(c) Motion for Judgment on the Pleadings. After the pleadings are closed—but early enough not to delay trial—a party may move for judgment on the pleadings.
According to rule 12(d), this is not the same as a motion for summary judgement under rule 56 (with all that entails) unless the court has already been presented with matters outside the pleadings.
Your question was about rule 11. I don't think your scenario would violate it. Under rule 11b:
By presenting to the court a pleading... an attorney or unrepresented party certifies that to the best of the person's knowledge, information, and belief, formed after an inquiry reasonable under the circumstances...
(1) it is not being presented for any improper purpose, such as to harass, cause unnecessary delay, or needlessly increase the cost of litigation;
(2) the claims, defenses, and other legal contentions are warranted by existing law or by a nonfrivolous argument for extending, modifying, or reversing existing law or for establishing new law;
(3) the factual contentions have evidentiary support or, if specifically so identified, will likely have evidentiary support after a reasonable opportunity for further investigation or discovery; and
(4) the denials of factual contentions are warranted on the evidence or, if specifically so identified, are reasonably based on belief or a lack of information.
It doesn't actually say in there that the defense must investigate the sufficiency of the plaintiff's claims (although that's obviously something the defense would ordinarily want to do.) The part about making sure "the claims, defenses, and other legal contentions are warranted..." relates to the claims being made the party in question, not the ones being made by the other party.
I can't think of any "pure purpose" one would have in filing an answer when a motion for dismissal is warranted.
Depending on the circumstances, a party might have good reasons to not make every claim they think they're entitled to make. Perhaps they aren't sure about how the court will rule on their motion to dismiss but like their chances at trial. (Indeed, if it's a certainty the court will dismiss, then perhaps Rule 11 sanctions are in order for the plaintiff, for filing a case that was not at all warranted by the law.) Drafting a motion is time the attorney has to spend, which is an expense for their client, and it may or may not work. But maybe their motion to dismiss Count D uses the same theories as their motion to dismiss Count A, and it's now worth it to make the argument. And maybe now since the court ruled with them on Count C they're more optimistic that the court will also rule in their favor on counts A and D.
If the defense delayed this motion solely to "harass, cause unnecessary delay, or needlessly increase the cost of litigation" then Rule 11 would be violated. But that seems unlikely. Look at the context. They're making a motion on the amended complaint. That's still rather early in the process. Given that a brand new count was added, an earlier motion to dismiss count A would not have resolved the litigation anyway, so there was no real delay caused. The costs for either side have not been significantly increased, either.
Also note the phrases "to the best of the person's knowledge" and "reasonable under the circumstances". The defendant only has 21 days to file a response after being served, and they might not even have an attorney yet when that clock starts. How much inquiry is reasonable in that time frame, especially when responding to a multi-count complaint?