Could you please ensure that you are not running into 103652 - Default display precision of PIConfig may cause event edit failures
PIConfig displays sub-second timestamps to 5 decimals. Timestamps have a precision of approximately 6 decimals therefore, by default, the displayed timestamp may not match the actual timestamp. Workaround is to set time display precision to 7 with following command: @timf 7.
If you are interested in exploring other deletion methods, refer to 3065OSI8 - How to delete archive and snapshot events
I think it will be difficult to determine what exactly is going on without being able to see the piconfig commands you're executing to get this error. In general, I would suggest calling into Tech support when getting an error with piconfig as they're notoriously difficult to troubleshoot
That being said, the first few things that come to mind (without knowing your commands) are do you have the correct table selected? Are you in delete mode? And are the columns in the correct order for the CSV.
Also as a general rule I would recommend using the Powershell tools for deleting tag values nowadays. The Powershell tools are capable of supporting buffered deletes with the AF SDK buffering (i.e. if you delete a value, you can delete it on both members of a collective simultaneously rather than one at a time) whereas PI SDK buffer doesn't support this. If you don't have collectives or already have a script you're using feel free to ignore this, but long term this may be a better solution.