There shouldn't be any problem with sending the amended return even though you didn't receive the original refund. The reason it is recommended that you don't is because you don't want to have to amend again if there is a problem found during the processing of your original return. So, it shouldn't have a practical effect on the processing of either return, but could open you up to a bigger headache down the road if a problem is found.
The IRS was holding all refunds that claimed EIC or Additional Child Tax Credit until at least Feb 15th, so that may have been what was really the hold up (I looked at your other question). If so, then you should see some movement on your refund status within the next week or so. Also, it takes at least 3 weeks (and probably longer at this time of year) for an amended return to show up in WMAR, so I wouldn't worry too much about that right now. But, they will cash your check much faster (of course).
