Rolled back to 3.4
I just had a (multi) split (using the split button) go
Wrong 
t times in a row (I aborted and grabbed a fresh Calibre converted file).
Split-off files ended up at the end of the list, the manifest was missing/name not updated files. Way too painful, but I repaired the damage to Flightcrew's standards
BTW The first time I launched Sigil from Calibre (open With).
The second time I shut down Calibre and opened Sigil and loaded the book.