This problem of inconsistency between IT 2001 and IT 2006 (deductions) is common.
Report RPTKOK00 is run to identify/report inconsistencies. If there are any, it provides a choice to fix the problem.
Choosing this leads to running RPTBPC10 to fix records in IT 2006, PTQUODED table and IT 2001.
Sometimes the first report may not identify any (as I have found many times for some of my clients). In this case, an alternative is to delete/recreate or re-save the absences starting from the earliest)
see link
Transactions and Reports in PT - ERP Human Capital Management - SCN Wiki