To follow this up and add what I just discovered. It appears between 5.3 and 5.4 some stuff changed in the build.cs file. I diffed a new build.cs from lyra with my old one and there was 2 small changes.
Line 28 from “Target.DefaultBuildSettings = BuildSettingsVersion.V3;” to “Target.DefaultBuildSettings = BuildSettingsVersion.V5;”
and
Line 248 from “catch (JsonParseException ParseException)” to “catch (Exception ParseException)”
I made those updates and it fixed my project that was based on Lyra