fdt_load_dtb_overlays was written to unload previous overlay when a new valid one is come across. fdt_apply_overlays further down is written to iterate over all .dtbo's currently loaded and apply them one-by-one. Correct fdt_load_dtb_overlays to stop dropping valid overlays that were previously loaded and match expectations.
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Did you test multiple overlays targeting the same node ?
Last time I talk to gonzo@ about he came to the conclusion that we need to update libfdt in our tree and use their overlay implementation.
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These are two independent issues: inability to modify same node and discarding previously loaded dtbo's. I think the latter was just a case of poorly applied copy-patse.