Upgrading only works between the last two releases, 4.4->4.5 and 4.5->4.6.. upgrading from 3.7 to 4.6 is unsupported.
The best method of updating this system would be to preform a clean 4.6 installation and migrate the previous configuration manually (..from a backup).
PF syntax has changed over time, copying 3.7 pf.conf verbatim will not work.. you will have to make some changes, the
PF FAQ and man pages can help you with this.
Feel free to ask additional questions, we'll certainly try to help make it easier for you.