Hello Thanga,
found the solution... don't ask me why I didn't find the support note 2057897 at 1st view... this is exactly my problem and the solution. And it fits to our patch-lvl.
Attached report "SBAL_DELETE_ORPHAN_MESSAGES" of the support message seems to work as described, it deletes orphan entries of BALDAT.
Sorry for circumstances and thx again. Hope this helps others with similar problem (seems it is for all SAP systems using BALDAT, not only SCM-system!!!)
Best regards
Harald