When upgrading a package say vsftpd, I used port install. After newer
version is installed, I have both newer and older versions being listed
if run pkg_info. The newer version works fine.

You can use portupgrade instead, which should deinstall the old
version, then install the new one. You can't install the new one
before the old one, so there will be a brief period of time between
the make deinstall and make reinstall that it may not be available.

Also keep in mind, if you are upgrading something like mysql, you
should update pkgtools.conf to restart it afterwards to minimize down
time (and so you don't have to remember to restart it). You can look
for the AFTERINSTALL section in pkgtools.conf for how to do this.

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