Technically we should not be clearing anything from the table. If for some reason you have to clear the an entry you should do it from SM58.
How it works:
When SAP comes across a tRFC call, instead of executing the call it writes an entry to ARFCSTATE table. Same is the case with qRFC and also update task. But for update task the table is different.
Once SAP comes across a COMMIT, it then starts processing all the update task and then looks into ARFCSTATE. If it finds an entry corresponding to the LUW which issued the commit, it then processes it. If its successful, SAP automatically removes this entry from ARFCSTATE.
Thanks,
Vikram.M