Yes, but you need to do some pre-processing. You can do this either in Excel or in a temp Filemaker file. Add a column for IndividualID and fill it with serial numbers. Then add 20 calculated columns along the lines of =
If ( Column B = "Y" ; 1 )
If ( Column C = "Y" ; 2 )
If ( Column D = "Y" ; 3 )
Import this into the join table 20 times, each time importing the IndividualID and one of the calculated columns.
Ok. I think I got it. Should I be seeing blank records for people who don't match with the company? I assume that I purge those, leaving only the ones that are linked.
Should I be seeing blank records for people who don't match with the company?
Yes (sorry, I should have mentioned that). You could prevent this by using field validation, but for a one-time conversion finding the join records with no CompanyID and deleting them would be easier.