simply test it. It depends on too many factors, so that there is no simple answer. 4000 "entries" (records) actually does not sound like a lot, but as I said, that is not the only factor....
So: write the routine that does the updating and test it not as a cronjob but by running it manually.
Experiment a little to make it more efficient - or come back here with your code if you feel you need help optimizing it.