If you use Outlook 2016 with current updates (with the new New Account wizard), it *should* only get new ones.
That is how it worked a couple of weeks ago for a client who had 40,000 messages on the server. If the data file is named using the email address (example: rkr3@domain.com.pst) and its in the default location (documents\outlook files), auto account setup should use the old pst. If you are concerned it won't (or the pst is named differently), click the option for manual setup and try selecting a pst - if the Browse button doesn't work and the pst name is your email address, it found the old pst. At least that is how it was for my client.
After starting outlook, i watched the status bar and it said 'downloading 1 of 160', not 1 of 40,000. Had it said '1 of 40,000' i was ready to take outlook offline (Send and receive tab) and set up a rule to move mail received prior to the last time she downloaded mail.
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