Dear Sai,
The way to reorganize the Bdoc tables is to schedule background job for report SMO6_REORG2, as you already did.
To improve the performance, could you please try the following options?
1. Run the basis report RSRLDREL2 for relation table SMW0REL before running SMO6_REORG2 report. This will delete the object links for BDoc's.
2. Run report "RSMW0_CLEAN_TABLE_NEW" which will delete the obsolete entries ( which does not have corresponding entries in SMW3_BDOC) from SMW3_BDOC2 table.
3. Report SM08_FLOW_REORG can be used to delete the BDOCs which are processed.
4. The reorg job SMO6_REORG2 only clean fully processed BDoc-messages, but not "yellow" or "red" ones. BDocs in the error state are stored in the system for the correction of the problem. After the relevant BDoc message are set to "green" status the job / report reorgs the relevant tables. Please check SMW01 to see how many such BDocs exist in your system. Change the status of unwanted yellow BDOCs to 'green' by marking it as complete in SMW01 and then these bdocs will be available for deletion.
5. Please ensure that indexes are updated regularly as described in note 707820.
6. Please also consider note 1138051 - Deactivation of BDoc to Object links
7. Please schedule the report as background job. The report SMO6_REORG2 calls many different reports and you can see the options for reorg different objects. You can define variants to separate the options in different jobs.
Best regards,
Ellen