Hello Shiju,
this is a just a shot in the dark but for starters can you check the following query?
select mcthismskey from mxi_link where mclinkstate != 2 and mcthismskey in (select mskey from mxiv_dirty_mskeys) and mcthismskey not in (select mskey from idmv_Value_basic)
This query should deliver all entries (users) that are supposed to be reconciled, have any active links within the system but were somehow deleted and therefore cannot be found.
Best regards
Tobias