I just recently updated my Logos software. I believe I had version 6.6, now after the upgrade I have 6.8. I discovered after the update that it had deleted at least four fonts that some of my Paratext projects used.
Ezra SIL: Hebrew font used by the source language window
Galatia SIL: Greek font used by the source language window
Charis SIL
Sheherazade.
There is a Logos support document that hints at this problem. I think what happens is some versions of Logos included these fonts as part of the installation, now they are no longer part of the installation, and the update process removed these thinking they were traces of the earlier version.