OK. I have changed the processing of the teams import to not recreate the teams.dat but to load up the existing one and only alter the records for those listed in the CSV file.
This gets round the integrity issues that getting rid of the 'ghost' teams brings in.
The link is at
http://www.bourtonville.co.uk/OOTPEditor/publish.htm
So, one further caveat to editing the CSV files is to make sure that you do not under any circumstances alter the team id numbers.
Also, if you open teams.csv and make changes and then save it back as CSV open it up in wordpad or notepad and make sure that each line ends in either ,0, or ,1, (unless you're running an historical league in which case each line should end in ,0,something or ,1,something)
Errors have occurred because the line doesn't have enough commas in it.