If by history file you mean you created the FYE archive, then deleting them in the current year will not affect the archive.  However, if you only archived payroll, that is not the case.

I recommend changing their vendor type to 999=inactive.  You can verify if they are connected to any job costs by doing a journal, by job, and then selecting the vendor number in the criteria.

Run it for all jobs and see if it comes back with a match.  If it does you should not delete that vendor until those jobs are archived.