Starting February 1st, 2015, Apple will require all submitted games to include 64-bit support. Stencyl 3.3 includes 64-bit support, but any extensions will also need to support 64-bit, otherwise games relying on those extensions will not build.
In order to support 64-bit in your extension, you need to make a few simple changes on your end.
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1) Download Stencyl 3.3 or later.
2) Open up project/Build.xml for your extension. Below this line...
<set name="IOS_ARCH" value="-v7" if="HXCPP_ARMV7"/>
add this line
<set name="IOS_ARCH" value="-64" if="HXCPP_ARM64"/>
3) Open up project/build for your extension. Below this line...
../../../haxelib run hxcpp Build.xml -Diphoneos -DHXCPP_ARMV7
add this line
../../../haxelib run hxcpp Build.xml -Diphoneos -DHXCPP_ARM64
4) Rebuild your extension (using project/build).
Under ndll/iPhone, you should now see a 64-bit binary for your extension. Re-upload your extension in full.