Hi Lucas,
I suspect the older version of Thonny has ended up in "user site packages" directory and it takes precedence over the desired version in site-packages. Perhaps you have installed a plug-in via pip?
Anyway, I suggest you open Thonny's plug-in manager (Tools => Manage plug-ins) and select "thonny" from the list on the left. You should see where the package is installed to. If it ends with "/Python/Python37/site-packages" and the version of the package is "3.1.2", then you should uninstall this copy of Thonny. After this you should still see "thonny" in the list, but now it should be the newer version.
Best regards,
Aivar