Processing of IT 2001 includes updating of the abs hrs/days, etc in IT 2001. The enhancement should not try to update these fields.
If you wish, you can enhance or use the user exits to modify for example, the absence hrs calculation. Go through the user functions/exits/badi's etc in MP200100 and see which is relevant for your purpose.
Also there is a good amt of info in the links below:
User exits and BADIs in the PT area - ERP Human Capital Management - SCN Wiki
Not sure if this will help in your scenario:
Absence Counting user exit or BADI
Further, if you have activated IT 2001 for decoupled infotype framework (DIF), then the same functions would be used for validation, PBO/PIO, user changes, etc. Otherwise, it would be more efficient to call the same routines for both ESS and R/3 front end changes.
See links re:DIF
Weblog42: Decoupled Infotype Framework #1: At a glance
SAPexperts | Avoid Data Inconsistency Between ESS and PA30 in ECC 6.0</title> <meta …
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DIF Time infotypes: Availability of time infoty... | SCN
Decoupling Infotypes - Developing an Infotype in Personnel Administration - SAP Library