| where strftime(StartDate, "%Y-%m-%d %H:%S") > Date
the code above parses Hour : Second which doesn't make sense
also, try this
| eval EndDate = strptime(AcceptedDate . " 00:00:00", "%Y-%m-%d %H:%M:%S")
| eval StartDate = strptime(trans_to_inprogress_date . " 00:00:00", "%Y-%m-%d %H:%M:%S")
EDIT
if above doesn't work because you mentioned the time format looks like "2018-11-16T14:10:20.969Z", try this:
| rex field=AcceptedDate "(?<date_ymd_ad>[^/]*)T(?<date_hms_ad>[^//]*)."
| rex field=trans_to_inprogress_date "(?<date_ymd_ttid>[^/]*)T(?<date_hms_ttid>[^//]*)."
| eval EndDate = strptime(date_ymd_ad . " " . date_hms_ad, "%F %X.%3N")
| eval StartDate = strptime(date_ymd_ttid . " " . date_hms_ttid, "%F %X.%3N")
| eval DateDiff = tostring(round(EndDate - StartDate, 3), "duration")
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