It seems like there's a lot of mixed perspectives on what is functionally happening! This was tested with spells and wildshapes.
Favored Souls -> Polymorphed -> Benefits from their Class Feats, resisting the selected energy type.
Resist Energy -> Polymorphed -> Benefits from the feat, resisting the selected energy type.
Warlocks -> Polymorphed -> No benefits against selected energy types.
Far as I'm aware, Favored Souls and Warlocks both use a similar setup (not functioning like Resist Energy, not stacking with items due to limitations). Warlocks are being affected differently, so I thought to post it.
"...gains all extraordinary special attacks possessed by the form but does not gain the extraordinary special qualities possessed by the new form or any supernatural or spell-like abilities." - Polymorph
"The creature retains the special qualities of its original form. It does not gain any special qualities of its new form." - Alternate Forms
Retaining resistances from feats post-polymorph shouldn't be considered a bug in my opinion, as you are already denied special qualities from the new form, nor does it say you lose any you already possess. You get to keep all your other feats, too.