It seems to me that the problem is caused by the notes crossed over to the left hand stave. Unfortunately, it’s not sufficient to move those notes back to the right hand stave, but you also have to delete them to make split flow work as expected.
I did as you suggested and it works correctly for the first few bars. However, the rest of the score has several cross staff notes, and all of them are corrupted or missing. Does this means that I have to move all cross staff notes back to their original position before splitting into flows?
Yes, here it is. I deleted the beginning and end. It is only a section of the piece around the area where I trying to do the split flow. Also to explain further, this is from an import from an xml file made by Sibelius 8.6.1 - and I have not started making any major layout edits after importing. section from Two Toccatas.dorico.zip (301 KB)