The possibility to treat missing observations is mentioned explicitly in 
Giannone, Reichlin and Sala JME (2008) for the case of forecasting the 
factors when some of the time series from which they are extracted are 
missing in the context of nowcasting GDP using a DFM model. I would also 
be interested to know if this is also possible to be done backwards, 
that is to extract the factors in the part of the sample where some of 
the time series are missing, and how (I guess the way would be the same 
no matter where one goes, forward or backwards).
Many thanks again.
Andreas