Retaining filter state for processing data in chunks
You can use the filter function of matlab with initial conditions with the following syntax: (excerpted from Matlab 6.0 command window help)

[Y,Zf] = FILTER(B,A,X,Zi) gives access to initial and final conditions, Zi
and Zf, of the delays.  Zi is a vector of length MAX(LENGTH(A),LENGTH(B))-1
or an array of such vectors, one for each column of X.


Hope this helps.