Thank you!
What I’ve decided to do is use one pipeIn for the main bulk of data.
A second pipeIn is used for the remaining data. The first 4 bytes define the number of valid bytes to follow. The first 4 bytes also hold flags to be written along with the last valid data.
The data buses from of the two pipIns are then multiplexed into a FIFO.
I am assuming that the first pipeIn will be complete before the second starts!