Everyone in Yr9 will be new to the Senior School - no-one will have done Yr 7 and 8 in the Senior school, but presumably in the Junior/Prep part as yours will, or possibly elsewhere for 13+ entry, so in that sense no-one is disadvantaged. If this is one of the big public schools, this approach is very common and 11+ entrants join the Prep for 2 years.
As everyone starts Yr 9 new I can't see any disadvantages. The difference to soending Yr 7 and 8 in Prep probably is more afternoons of games per week, more leadership opportunities, possibly more trips.
Do they prepare to do Common Entrance or have they scrapped this? If not following a CE curriculum, what is the curriculum? How large is the year group compared to what it will be in Yr9?
Many public schools only start in Yr 9 so all children have to be elsewhere beforehand for Yr 7 and 8. Most will be in Preps, either having been in the Prep since 4 or 7 or having joined at 11, or in a few cases, have spent Yr 7 and 8 at a state secondary. So what you describe is entirely normal for this kind of school and soending yr 7-8 in the senior part, just not part of that system.
There is a move for some independents to lower the entry age to 11, but this is usually if there is no feeder/owned Prep and is a way to avoid pupils going elsewhere,N when even for 13+ entry, most testing is now done in Yr6 via 11+ deferred entry.