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This happens in FL 5.0.3 for Mac:
About half of the kerning is lost (mostly the pairs that are not classes) when having OT-classes also in the font.
The kerning looks OK in the metrics panel, but when generated or updating the kern feature it shows that all kerning is not present anymore.
If I take away the OT-classes, the whole kerning is back again when I generate "kern" feature.
In this case it was smcp1 + smcp2.
Could anyone try and see if they have the same bug?