This looks like a bug.
Paratext should write to the user.config file a ProjectFontOverrides section, but I guess it writing the override for the Joined Named. (ie. HEB/GRK) instead of writing for for the HEB or GRK projects.
One could fix this by manually editing the user.config. (but the file is a little hard to find)
Here are some steps that should work:
1. Change the font for the resource. (like you have done.)
2. Close down Paratext.
3. Locate the user.config file.
In an explorer window navigate to c:\Users\{YOUUSERNAME}\AppData\Local\United_Bible_Societies\
There should be one or more Paratext.exe_Url_?????????? files.
open the one with the latest data modified.
Then there should be one of more version folders. Pick the one that matches you Paratext version.
open the user.config in notepad and search for <string>HEB/GRK</string>
Change the HEB/GRK to GRK (if your trying to change the GRK font) and save the file.
4. Reopen Paratext and the GRK font should have changed in the HEB/GRK project.
And/Or use the "Give Feedback" option to report the bug.
Some old info about this here:
https://support.bible/1585/hack-to-change-fonts-paratext-8-uses-for-resources