See clip from Attorney Rajiv S. Khanna's conference call video that addresses this question.
If you file for your H-1extension you are allowed to travel. You are allowed to travel even when your H-1 transfer is pending. A few things to keep in mind when you do - is are you maintaining status etc etc., but travel while transfer or extension of H-1 is pending is allowed. The question is when you come back your I-94 changes and that is not a problem. That should not cause any delay and I don't see any need for any amendment. The fact that your H-1 is taking so long is most probably not related to this issue. But if you want you can double check with the USCIS customer service. I always advice that.