Dear Julius,
By default, the batch job will be triggered immediately after you press the "START" button if you choose "merge now". Of cause, you can monitor the status of the job in transaction code SM37. The Archive (BUT000-XDELE) flag will be set after the successful execution of batch job BUPA_REALIGNMENT (program CRM_BUPA_REALIGNMENT) during account merge.
Thanks,
Julin Xin