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So, the problem occurs when deploying to the default EAP server created by the JBDS installer. It turns out it doesn't create the temporary deploy folder usually created when manually creating a new server, making subsequent deployment of zipped resources fail.
Attaching a patch fixing the issue. It simply checks and created the missing temp deploy folder before zipping.
This fixes this particular issue but I have no guarantee similar error won't occur elsewhere in the code.