Several colleagues and I have found that after the upgrade to 6.3, our other programs that display Greek or Hebrew text couldn't find the fonts they were using.
I appreciate that Logos has documented the issue. https://www.logos.com/support/logos6/windows/missing-fonts
I would encourage Logos to do more -- if the installer cannot tell whether fonts were installed manually or by an earlier Logos version, how about having it give a warning, like this:
"The following fonts
<list names>
may have been installed by a prior version of Logos. Logos 6.3 no longer requires these fonts to be installed into Windows since they are bundled into the Logos application. Do you want to remove these fonts from Windows?"