HI Sourabh,
This doesn't seem to be correct behaviour. When you say that you run SPL check against delta file, I assume you are talking about scenario C1 and C2. These two scenarios excludes existing blocked business partnera and those placed on a positive or negative list.
Unless you run B1P scenario, positive list of BPs should not be affected.
can you please double check which batch jobs are running after delta load.
regards,
Kul Vaibhav