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If the process is in error, then you need to abort the process - WF_ENGINE.AbortProcess is the API to call.
If the process has any child flows, then these must be complete before purging can take place - if they are running, then you need to abort them using the same API.
Once the process and all the child processes are complete, if they have been completed by the value of the persistence value for the Item Type, then you can purge them using the WF_PURGE APIs.
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You can follow WorkflowFAQ.com advice but check if, as per your Apps release, the procedure has the parameters 'verify_lock' and 'cascade' (these were added as a sort of enhancement request). If you have them then pass FALSE and TRUE respectively. This will take care of canceling the underlying children processes. So basically you will:
create a cursor to identify those unwanted workflows
loop through the cursor and call WF_ENGINE.AbortProcess(iitemtype => <cursor.item type>, temkey => <cursor.item key>, verify_lock=> FALSE, cascade=>TRUE);
Those items will be removed by the purge when their persistence time has expired.
Remember to do this first on a TEST environment.
Is there any permanent fix for this problem , what is the actual reason for this?