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Assuming you're building a dissector plugin, the libraries that your plugin will link with is set by the target_link_libraries() statement in the CMakeList.txt for your plugin. Normally this will include epan which is the link to libwireshark. If you have anything odd here, you'll have to fix that.

Just clutching at straws, can you confirm you are using a separate build directory for the 32 and 64 bit builds? You can't build both in the same build dir, both builds can share the same source dir.