Partnership - no UTR issued - now ceased!

I have clients who became a partnership in June 08 but did not register with HMRC as a partnership - both were self-employed, so were already in SA.

We completed the partnership tax return with 99999 99999 reference as at that time we didn't know whether a reference existed. The partnership ceased in October 2009. HMRC have not accepted the paper partnership return as there is no reference and are asking us to write to Longbenton CAAT team.

Do we just complete a CWF-1 for each partner and at the same time tell them the partnership has ceased? Seems a waste, but we will need to file an 09/10 partnership return.

Also, what are people's experiences of penalties for not registering within 3 months? I've had no penalties imposed in 10 years - then one was issued last month....

Thanks!