I have done some tournament directing and my assumption (dangerous I know) would be that both day 1"s would play down to the end of an appropriate level, regardless of how many players are left - probably the 2000/4000 level.
This would enable day two to start at 3000/6000 and no players getting an advantage out of differing finishing blinds.
This method will not take into account the number of players left each day (you may have 17 from day 1a and 15 from day 1b etc), but does seem the fairest.
I may be completely off the mark however, but I"m sure Des will put me straight........
Ian