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Long Time of commissioning. That is what confusing!
Well DCS have the facility to modify the programming during the running/execution. You can modify the program without any problem. Whereas, in PLC we have to reprogram and then restart it, whenever possible.
Just to get the point where rectification is required, plan the job and make it correct. Thats it
Simple answer
Correct it
It is the duty of an engineer to report and where possible to correct any errors.
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first of all you have to raise site query describing the error and through the management of change process the error can be evaluated, corrected and followed.
Trace out the file where the error has occured, For example, if it is a control drawing file in DCS , trace out the file from ur message. Create a new file with the same name, rewrite the logics using function blocks or ladder logics or diagrams, Overwrite the old file with the new one where the Project files are stored. Then give an offline download & once u have checked it go for an online download.
I recommend u always keep a back up for all ur files once it works so it would be easy for restoring it in future.
Just restart cpu instantly.
Simply, you have to confirm the required to modify this specific error, if the correction required to be done offline then you have to wait until next shuldown, or may not required offline which you can corrected online.