My console has two separate file systems on it and I have no idea why.

[/xbox]

Hey everyone I'm back again except this time I need some wisdom.
I'll explain real quick on what I've done leading up to this point. I wanted to delete my DVD drive since its nearly shot and can barely read any discs despite servicing it. I looked in my little bios collection. found a 128mb bios, patched it for my HD+ and it flashed successfully on my open xenium.
Now here is where things get weird. I used FatXplorer to format my WD Velocirapter 10,000 RPM drive. everything seemed great so far. I copied over all my data from my original hard drive and it boots just fine in testing.
Today I wanted to finish the set up of my HD+ software and I boot my console to the open xenium menu and connect via filezilla. All except my E partition are empty! I thought that is weird it should have a decent amount of data on it.
I boot the console from its new BIOS and sure enough all my files are present so I refresh Filezilla and I see two entire sets of partitions. If i boot to the open xenium I can only see one set thats nearly empty and I can copy data to it to my hearts content. If I boot the BIOS it shows both sets but the partitions that contain my original XBOX data are accessible however any attempts to upload data to the console are met with an error message simply saying error 550 could not create directory. I guess its set to read only.
I honestly have no idea what to think of this, I wouldn't object to wiping the drive again and setting it up but what caused this? Why can the mod chip only see one set of partitions while the console can only see the other set? is this a limitation of the 1tb drive? is it because its an "advanced format drive" witch FatXplorer gave me a warning about and showed recommended partition settings that I followed.
Did my mod chip make these partitions because the drive isnt locked? Does it need my HDD key?
​
My biggest question is with what functionality is left of my DVD drive should I burn some kind of recovery disc and rebuild my consoles filesystem and then recopy the data over to it? I don't really have anything worth keeping. If I should burn a disk is there a recommended one I should use and what DVD type should I use? I have some I use for Xbox 360 Recoveries on my XDKs that are just generic discs if those would work.
Thank you all in advance for your advice and suggestions. Admittedly I didn't expect to have this odd file system problem

submitted by /u/ViolentLambs
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