Considering the "being a debug xbox", I can say yes, it should work without issues.
The problem will be the Splinter Cell Exploit. If you restore your C and E contents (after turning the shadowc off), you will overwrite the M$dash exploit on the C partition. If the backup came from an xbox with a different kernel version, the softmod won't run on the new xbox.
If you have the kernel independant softmod, there shouldn't be a problem.
Also, if you don't overwrite existing files on the C partition (like the ernie.xtf and xbox.xtf), the kernel dependant files won't change, so the softmod should continue to work.
As always, make sure you have the xbox eeprom.bin on your pc before you start such drastic changes to your xbox C and E partitions.
I never found a tutorial that described how to turn your xbox in a debug unit using that phoenix bios loader. I did it myself that way, and I can confirm that it works fine. The triple boot ndure softmodded M$dash can hapilly live together with the debug dash.
I do remember having issues with free space on the C partition in the beginning. I can't remember anymore if erasing the filler files in the c:\shadowc folder was enough to do the job. I might have recompiled the nkpatcher as well so that it looked for the shadowc on the E partition instead of the C partition.
The biggest problem is if it doesn't work right away. You have no clue upon what's going wrong.
The procedure also works with the original M$ debug biosses that come with the recovery cd.
You just couldn't run retail xbe's with those biosses. You also couldn't add the F partition to the xbox neighborhood.
Never run the recovery cd on your xbox. It will erase the xbox eeprom and will try to flash your xbox tsop with it's debug bios. If the write enable points aren't connected on your mobo, the tsop flash will luckily fail, but your xbox still won't boot anymore due to the eeprom erasure.