Thanks for your reply.
If you're hoping to insert the rows as new rows rather than updating the existing rows, then unless you reassigned the PK for the new rows, you would probably encounter duplicate key violations when you ran the script. In other words, if the default is to update the row with ID 15, if you instead tried to insert a row with ID 15 then the script would fail as ID 15 already exists.
There isn't a way in SQL Data compare to reassign a primary key value, but you could try using a different comparison key in the project and also exclude the column you were using as a key before. If the PK column is excluded from the project, then SQL Server will assign a value when the row is inserted, but how this would match up with any other related rows is difficult to say.
It sounds like you're almost wanting to merge data, which is pretty difficult to do with SQL Data Compare, as it's primarily a synchronization tool.