I had the same problem but I found a home made solution to overcome this. Maybe there's a better solution ...dunno:
1-you should have files names something.000 something.001 etc...
you have to rename every file to make them begin with *.001 extension and so on.
So you just rename your original something.000 file to something.001, your original 001 file to 002 etc.
2-you have now files called something.001 something.002 etc. Go and get a freeware called HJsplit (type under google you'll get it). This prog joins splitted files starting with a 001 file (that why I renamed the files in 1- ). Run the prog, choose JOIN and point the prog to your renamed something.001 file (originally something.000 file), and start joining
3-after a while you get a file called 'something'. That is a combined file of your older files. Rename that file to somethnig.iso. And there you are, you can load that anywhere daemon or whatever...
I guess this thing works because all CloneCD does is reading bit by bit the dvd and splitting to several files.
keywords: what to do with clonecd *.dvd *.000 *.001 *.002 ... files