Dunno if you're still having a problem with the HDDs, but if so this information might help to know.
NEVER, EVER restore a 20GB or 60GB drive image to a BEVS drive. I tried it using Xplorer360 extreme 2, and afterward my BEVS saw the same problem-- Not detected in the 360. Now if I read your issue right, that's what you did. Basically, if you were to use Xplorer360 extreme 2 to dump the hddss.bin from the BEVS drive and compared it to the hddss.bin you ORIGINALLY flashed it with in a hex editor (ie. hex workshop), they look completely different. The hddss.bin that now comes from the BEVS drive is identical to the 20gb drive image's hddss.bin (don't believe me? open the image in a hex editor and go to line 2000. sorry if that's not correct lingo for it; i'm a little new to hex).
Here's how I got my BEVS detectable again:
At the time of the problem, I still had the original UNDO.bin in the folder I had hddhackr. I made backups of every file hddhackr made in the process of flashing just to be safe, so before you continue, if you haven't I suggest you do the same. Now what I did was loaded up hddhackr with my BEVS drive, and tried the usual "hddhackr -f". hddhackr reported that the drive should be readable in the 360. I knew this not to be true, and I found my proof of why from examining the hddss.bin dump from the drive just before trying to reflash.
So, at this point i did "hddhackr -u" to "undo" the flash, because it was the only way hddhackr was going to let me reflash (remember, my UNDO.bin was the original UNDO.bin I had-- the one that would restore my drive back to normal). After undoing, i shut down, waited 10 seconds, booted up and went to "hddhackr -f" and reflash. I had the 120gb hddss.bin I originally used to convert the drive to 360 compatible state in the folder. hddhackr asked me if I wanted to create an UNDO.bin, and since I already made a backup of my UNDO.bin, I said sure. hddhackr refused to flash it due to an existing UNDO.bin in the folder. I did "hddhackr -f" again, but this time without creating an UNDO.bin. Popped it into my 360 and it detected! Only odd thing is it said I had 3.5GB left of free space. I pressed the Y button on the 360 and reformatted the drive, and it showed 107GB free again.
Now what to do about partition 2? Absolutely nothing, because despite how much of a mistake it was to restore a 20GB image to a BEVS drive, it actually created partition 2, and is completely visible on the drive (hell, go check it in Xplorer360 if you don't believe me). At this point there is nothing more you
need to do to your BEVS drive. Works, partition 2 is visible... life is good. But if you want to get data from an old HDD onto the BEVS drive, I highly suggest you manually copy the folders off of the old HDD into a temporary folder on your windows machine, then manually copy those folders onto the BEVS drive. I wouldn't take any more chances with the restore image feature, even if it seems safe.
Hope this helps you out, but if not, someone else will find it and it will hopefully fix
their problem.
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