I thought this should have been handled on installation, but maybe your case was unusual.
There are example udev rules in the installation, although when I run "dpkg-query -L weewx | grep udev" I get multiple conflicting examples - even on a fresh install, let alone an upgrade.
All the examples seem to rely on serial port via a usb adaptor, so if you have a real com port then perhaps that is why.
I don't know where the 99-com file comes from, but it sounds like a default catch-all.
Generally you should have a separate, specific rule file, something like "20-vantage.rules", to ensure it remains after an update.
I tend to give tighter permissions, such as 0660 to reduce the possibility of other programs poking their noses in.