You may not be familiar with the less-common "election by original presentation," in which the Examiner elects the claims. Now, it's not as bad as it sounds – this can happen only in limited situations, and the Examiner can't just elect any subset he wants.
Here's the deal: the Examiner is allowed to use election by original presentation (described in MPEP § 821.03) when you add claims that are directed to a different invention than the one you originally started with. The idea is that the Examiner already searched the original invention, so you can't pursue the new invention in this application, even if you want to. So the Examiner elects the claims directed to the original invention and withdraws the other claims. The MPEP instructs the examiner to use this form paragraph:
Newly submitted claim  directed to an invention that is independent or distinct from the invention originally claimed for the following reasons: If you disagree with the Examiner that the new claims are directed to a different invention, you have the same recourse as for the standard restriction requirement: you request reconsideration and provide arguments why the restriction is improer, and then you petition if that fails.
Since applicant has received an action on the merits for the originally presented invention, this invention has been constructively elected by original presentation for prosecution on the merits. Accordingly, claim  withdrawn from consideration as being directed to a non-elected invention.
What is a "newly submitted claim?" Is it limited to new claims added during prosecution, or does it cover an amended original claim? I don't know the answer to this, but it makes sense to me that the Examiner could also use election-by-presentation when you make amendments to an existing claim. After all, we've all seen amendments that replace 90% of the words in the existing claim, right? How is that any different, substantively, than a new claim?
Not being allowed to pursue newly claimed subject matter as a result of election-by-prosecution by the Examiner is annoying enough – but there may be worse side effects. To begin with, you can get slapped with a non-responsive amendment if your response cancels the claims directed to the original invention and thus includes only claims directed a different invention. Here's the Examiner form paragraph, from MPEP § 821.03:
The amendment filed on  canceling all claims drawn to the elected invention and presenting only claims drawn to a non-elected invention is non-responsive. The remaining claims are not readable on the elected invention because .Worse yet, if you file an RCE in order to get those new/amended claims entered (the ones directed a different invention), and then the Examiner withdraws them from examination...you've wasted an RCE fee. You'll need to file those claims in another application, and you don't get your RCE fee back.
Since the above-mentioned amendment appears to be a bona fide attempt to reply, applicant is given a TIME PERIOD of ONE (1) MONTH or THIRTY (30) DAYS, whichever is longer, from the mailing date of this notice within which to supply the omission or correction in order to avoid abandonment. EXTENSIONS OF THIS TIME PERIOD UNDER 37 CFR 1.136(a) ARE AVAILABLE.
If the Examiner balks at your claims directed to a different invention, make sure that the Examiner actually issues an Office Action with a restriction-plus-election-by-presentation. What you don't want is a generic Office Communication simply informing you the response is non-responsive because the only claims in the case are directed to a different invention. (See the file wrapper for 11/300,970 on PAIR for an example of this.)
What's the difference? An important one: only an actual restriction requirement allows you to file the restricted-out claims in a divisional rather than a continuation, which in turn avoids protects you from a double patenting rejection.
I don't know how common Examiner election-by-presentation practice is. It's happened to me only a handful of times. But it is something to think about when adding lots of new features to your claims.