Dear Aditya,
You can load the data for all sales data-sources with different plant selections, but make sure, all the data properly filtered and blocked the sales posting at the time of of filling setup table.
And can run delta as usual.
And for the 2 new plants (what u described) , u have to fill the setup table for only those 2 plants and no need to delete the setup table data before filling setup table.
Bcoz data will be there for other plants.
And to keep in safer side, you can use DSO before loading data to Infocube.
Thanks,
Balaram