Sorry about the delay, this got lost in the holiday madness... I ran out of time (at least as much as I was willing to spend) to get pandas/notebook to work so mostly brute-forced it. In sum:
Import the original tab-delimited file to Excel (using data model/data refresh so I wasn't manually fixing the fields each time)
Do the work on my FC
Join the Excel table to my FC
Made a simple table-to-table model to rearrange/change field names so only the updated/required fields exported
Imported the csv back into Excel (since Pro can't directly export tab-delimited through models- not sure if 2.9 added that)
Exported from Excel to a tab-delimited file
Dumped it back into the Clerk's software.
I had to run the Clerk's data a bunch of times so even this semi-automation saved me some time.
Thanks,
Tycho