Christophe,
Thank you very much for taking the time to look at my files. And, apologies, because it seems I must have posted an incorrect liquid boundaries file. I hope I didn't waste too much of your time. The liquid file I'm using has correct inputs (Q(1), SL(2), SL(3), SL(4)) and is working just fine.
Regardless, I seem to have things working now. I took Riadh's advice (see above) and removed all but the velocity and free surface components from my selafin file and tried again - this time with success. So, it seems that the problem was probably related to the size of the hotstart file (now 2.5 GB before parsing the unnecesary information).
So, for the moment my problem is solved. However, I may run across this again if and when my velocity and free surface only selafin files become unwieldy. What I think I need to do is to create a single timestep selafin file. I've tried to do this in BlueKenue to no avail. I can't seem to find an obvious way to save or extract a single timestep from the selafin file. If I save/extract/calculate a single timestep for any of the variables and then add these to a new selfafin object - they lose their metadata related to time. If I update the time headers in the text file and try to add these to a Selafin file, BlueKenue crashes. I will mention this in a post I am working on for the pre/post-processor forum.
Thanks again for your time,
Tamsin