The general rule that an amendment cannot be entered in part and refused in part should not be relaxed, but when, under 37 CFR 1.312, an amendment, for example, is proposed containing a plurality of claims or amendments to claims, some of which may be entered and some not, the acceptable claims or amendments should be entered in the application. If necessary, the claims should be renumbered to run consecutively with the claims already in the case. The examiner should annotate the amendments by using the Strike-Out Line tool to cross out any refused claims or amendments.
The examiner should then submit a Response to Rule 312 Communication form PTO-271 recommending the entry of the acceptable portion of the amendment and the nonentry of the remaining portion together with his or her reasons therefor. The claims entered should be indicated by number in this response. Applicant may also be notified by using form paragraph 7.86.
¶ 7.86 Amendment Under 37 CFR 1. 312 Entered in Part
The amendment filed on  under 37 CFR 1.312 has been entered-in-part. 
When an amendment under 37 CFR 1.312 is proposed containing plural changes, some of which may be acceptable and some not, the acceptable changes should be entered. An indication of which changes have and have not been entered with appropriate explanation should follow in bracket 2.
Handling is similar to complete entry of a 37 CFR 1.312 amendment.