One option is to prepend the original fields before sending to the summary index...
| foreach _* *
[| eval orig_<<MATCHSTR>>=<<FIELD>>]
(You may want to only prepend the fields you actually need, and which get overwritten, e.g. host, source, sourcetype, instead of _* * )
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Just want to add, if your timestamp included milliseconds, you can use:
| rex field=diff "(?\d+):(?\d+):(?\d+).(?\d+)"
| eval dur = (HH * 3600) + (MM * 60) + SS + (MS / 1000000)
my timestamp had 6 decimal places for ms, so I divide ms by 1,000,000
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