Help needed: ReadyNAS NVX (RNDX4000) Restore to RAIDiator 4.2 - Empty /boot_flash

First off, your NVX cannot be converted to OS6,  It's a 32-bit unit, and OS6 is 64-bit.  There are plenty of warnings in the forum and elsewhere that trying to do so can brick your unit.  So it wasn't something you did wrong in the process, it's that you attempted it at all that caused your issue.  So if you get this sorted out, don't try again.

Second off, the directory boot_flash is not your actual boot flash unless you have manually mounted the flash device to that directory.  Unless you manually deleted it's contents, it should currently contain the non-bootable (by your NVX) OS6 image.  It's been a long time since I used an OS4.2.x system, but I think that's where it temporarily stores the flash content before re-booting and installing it on the actual flash.

While the warning is that this can brick your unit, typically it does not and all that's needed is a USB recovery with OS4.2.31.  If it really is empty, that will not restore your vpd file, so it still won't boot.  But that's the first step.  The vpd is an encrypted file that contains more than just your serial number, and there is no way to create your own.