Sales Update R42800 Performance

Hi Experts,

We are running R42800 which process around 2000 records in around 200 seconds.

but sometimes it process over 90,000 records due to which it takes many hours to complete.

on the log it showed only 1 warning-

RUN0000067 - Warning - ProcOpt Data Size Mismatch: Requested 612 is less than Retrieved 614 for App R42800, Version DAB0001.
Data Structure allocated successfully. This usually means items have been added to the template and existing
business function will function correctly.

Does this warning resulting in performance issue or how can we improve the performance ?

We also reviewed the log for any time issue but there no issue.