Yes format the partitions in ext4
Okay, so after a couple of hours I'm up and running, all systems a go. Here is what I did to recover as well as my key takeaways from this incident.
A little bit of history
Yesterday I found that my bare-metal Gen8 microserver had been automatically updated from 6.0.2-8451 Update 11 to the nefarious 6.0.3-8754. As I was running Jun's 1.01 bootloader, I soon learnt that my bootlegged NAS got bricked. My setup features two 4 TB WD RED drives hooked in a RAID 1 (Volume 1) array, a 3 TB WD Green as a Volume 2 array and a 120 GB SSD drive acting as cache.
I was able to find the device in the Synology Assistant, yet I was unable to access shares, apps or the admin interface.
What I did
Step 1. Panic. I had planned for hardware failure but not to the point where I could not boot the freaking rig at all. I realized that my NAS kept being detected as migratable and I was stuck in this migration loop for a while.
Step 2. Disconnect the SSD cache and the Volume 2 (the 3 TB WD Green). Used the Gen8's iLO interface to boot the management console and mount an Ubuntu 16.04 ISO. Booted the rig off of the Ubuntu image and fired up gparted (Unity icon -> gparted ->enter). In my case, the gparted info looked like below:
/dev/sda1/ - 2.37 GB
/dev/sda2/ - 2.00 GB
/dev/sdb1/ - 2.37 GB
/dev/sdb2/ - 2.00 GB
some unallocated partitions and the data partition which was 3.63 TB large were also present. Formatted the /dev/sda1/, /dev/sda2/, dev/ sdb1/ and /dev/sdb2/ as EXT4, then applied the settings, then rebooted. Fuck. Same bootloop between recoverable (settings lost) and migratable.
Step 3. Repeat step 2 but rewrite the bootloader from scratch using Polanskiman's tut here: viewtopic.php?f=2&t=22100. Just to land on the safe side for once, I got a new flash drive I had lying around and prepared the bootloader image. Booted the rig and installed DSM_DS3615xs_8451.pat from https://usdl.synology.com/download/DSM/ ... s_8451.pat (side note: before you start doing this, don't be stupid, delete all the downloaded images you might have in the download folder and start from scratch. It's gonna save you a ton of work if you know which file is which). Created the admin user and password and logged in.
Right after, I applied the 6.0.2-8451 Update 11 fix downloaded from http://download.synology.com/download/D ... 3615xs.pat.
Rebooted, fixed my DNS (i changed the MAC and serial number so my router issued a different IP than what I had leased until yesterday).
Step 4. Add the SynoCommunity Repo and install my previous apps (CouchPotato, Sickrage, Transmission and Headphones). Since it's 6.0.2, make sure that you have created the default users (couchpotatoserver, sickbeard-custom, transmission and headphones) prior to the actual app installation. Also grant the appropriate RW privileges on the folders they should have access to.
Reboot and profit.
Remember, next time don't take the leap of faith and make sure that you don't install updates that have not been green-lit by the community. Also, I was kinda impressed by the resilience of my setup. Not only that I was able to recover without losing any data, but I was also able to mount volume 2 and the SSD cache without losing anything on Volume 2. Of course, i formatted the cache drive without remorse.
Thanks everybody who have helped me get back on track. Good luck to everyone else who fell for 6.0.3.