Often, "EBOOT downloads" are actually game updates. You can use tools like PS3 Game Updater to download official PKG files which contain the EBOOT.
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This common error usually means the EBOOT is encrypted and cannot be read by your current firmware. Resigning it as a "debug" or "retail" EBOOT for your specific firmware version typically fixes this. Often, "EBOOT downloads" are actually game updates
Copy your downloaded patched EBOOT.BIN into USRDIR , overwriting the original. overwriting the original.