It worked until the deletion of the bootcamp partition. I deleted it via the drive utility and then did the same thing via the bootcamp utility. Both caused the external thunderbolt bootcamp to get to the black screen with cursor.
This is expected behavior. Apple hardware can only have one disk with an MBR which contains bootloader code, because there's no way for you to choose which disk to boot from like hardware that contains a real BIOS. You have to zero superfluous bootloaders.
Further I think you're better off with this level of nitty gritty experimentation and iteration to use real tools, i.e. you should become familiar with fdisk, gpt, and gdisk, and stop using Boot Camp Assistant and Disk Utility. The GUI apps blatantly obscure their true behavior. They are doing multiple things with a single click, so narrowing down exactly what is causing what behavior becomes immensely more difficult to figure out - and they do not restore the disk or partition states the way they once were, e.g. neither of them remove BIOS/MBR bootloaders from any disks.
Theory, when bootcamp is created onto the internal drive, I think a MBR is written to that partition to allow a bootcamp install/boot.
An MBR is present whether it's MBR only, or GPT. If it's a GPT disk, the UEFI spec says there should be a PMBR. That's an MBR with a single partition entry taking up all sectors of the disk, with ID 0xEE. It's there for legacy MBR editing utilities to see that the disk is entirely claimed for partition type 0xEE, rather than appearing empty, and subject to alteration. Newer MBR utils explicitly recognized type code 0xEE and will warn the user that the disk is a GPT disk.
Next, it might be time to stop using the term "bootcamp" because it's effectively a useless term. Boot Camp Assistant is a specific thing (with obscured behavior). However, "bootcamp" cannot be "created" on an internal drive. That's not what's happening, at all. When you use BCA, for the most part it's using:
diskutil resizevolume
First the JHFS+ volume is shrunk, the GPT is altered to account for the smaller Mac OS partition, the free space created is formatted FAT32, the MBR is then changed from a PMBR (a single entry MBR, with code 0xEE), to one that contains more than one entry. Apple goes for parity, i.e. they stuff the GPT and EFI System partition into the MBR's first entry as type 0xEE, then they stuff GPT partition 2 (Mac HD) into MBR partition 2; GPT #3 (Recovery HD) into MBR #3; and GPT #4 (FAT32 for Windows) into MBR #4.
When you use Windows to reformat that FAT32 volume as an NTFS volume, it actually edits the MBR to change the type code from 0C to 07. The GPT partition type code is unchanged (both because Windows ignored GPTs when booted in BIOS mode, and because the GPT partition type code for FAT32 and NTFS are the same, unlike in the MBR world).
You can achieve this hybrid MBR multiple ways, as there are no standards for them. You can do it manually with fdisk. You can do it with gdisk which has an explicit option for creating a hybrid MBR, with options. You can do it with gptsync which is a utility included with rEFIt and rEFInd - but it's kinda brain dead in that it only goes for the parity option.
If you need/want a fifth partition, you can run into huge problems because you can put five partitions in an MBR (but you can put 128+ in a GPT). Apple's tools basically puke, and overwrite a hybrid MBR with a PMBR as soon as there are 5 or more partitions. The tools do this without adequate warning. And it will make Windows unbootable until the hybrid MBR is recreated.
I saw this when I unplugged the thunderbolt before the internal partition was deleted and chose the "windows" partition at the option screen and it booted to a "windows" broken boot screen.
Apple's EFI scans disks and if it finds three true attributes on any disk: a hybrid MBR (defined as an MBR with the first entry 0xEE, and at least one additional MBR entry); one MBR entry other than the first entry has the active (bootable) flag set; there is bootloader code in the first 440 bytes of the MBR (sector 0); if those three things are true, it produces a hard coded "Windows" labeled disk icon. If you have two disks that fit this description, you still get one "Windows" labeled disk; the exception is it will produce a second "Windows" option for CD/DVD media with appropriate icon.
When you choose this option, EFI loads a CSM, which runs a BIOS, which in turn only understands MBR, blindly chooses the first available disk that has those three characteristics, and then blindly loads and executes the first 440 bytes of code in the MBR - the first stage bootloader. That then chain loades to additional bootloaders located within the Windows NTFS volume.
I'm thinking that apple now requires the bootcamp partition in order to boot to the thunderbolt drive.
What it would require is no other disk having a hybrid MBR or latent bootloader code in its MBR; only the Thunderbolt disk should have a hybrid MBR and bootloader code.
I fixed my thunderbolt mbr and bcd before the internal partition was deleted and as observed once booting into mac osx the bootability is broken.
Yeah I'm virtually certain this is because you have two sets of bootloader code, and we do not have a UI from Apple to choose which disk is the boot disk like on computers with a real BIOS and a BIOS setup menu.
AstroZombie138 is experiencing a different problem specific to the 2012 MBPs (I think, or maybe it's Mountain Lion I'm still not sure), where all of this functions as expected until he boots Mac OS X and that somehow breaks Windows bootability on the external Thunderbolt drive. And that's pretty weird.
Using dd to copy sector 0 through 34 to a binary file will copy the MBR (including bootloader code and tables), the primary GPT header and tables. Doing that before booting Mac OS X gives a snapshot of both partitions and bootloader info in a working state. Then boot Mac OS X, confirm that Windows boot is now broken, and take another copy of sectors 0 to 34, and then compare the two files.
If they're the same - well holy crap because that means something may be corrupting the bootloaders within the Windows volume and that would be pretty hideous.