Ok, I think I now understand how this all happened...
My sources.list file contained the word "stable" instead of "wheezy" which I didn't realize it meant Debian 8.0 "Jessie" (which OMV does not support). So, the reason there were "a lot of packages to update" is more clear now and I've done something I shouldn't have. Without realizing it, I just screwed up my whole system.
Now, I believe all my configuration files are still intact so... Is there a way to simply downgrade all packages to the latest stable version from Wheezy? I since changed my sources.list to "wheezy" instead of "stable" and ran "sudo apt-get update". This way I could just properly reinstall OMV and hope for the best.
If not, my second approach (and probably the recommended one anyway) is to restore my old backup (from March 14th) from the Backup plugin. It's one of those backups where grub.dd, grub_parts.dd, packages and uuids files exists in the root backup folder. I have read the restore guide, but I'm still confused by a few of the commands and how to properly do the restore process without messing the system further.
For the record, here's my block devices:
amaral@ATLASBOX:/$ lsblk
NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
sda 8:0 0 232.9G 0 disk
├─sda1 8:1 0 1K 0 part
├─sda2 8:2 0 32.8G 0 part
├─sda3 8:3 0 100M 0 part
├─sda5 8:5 0 9.3G 0 part /
├─sda6 8:6 0 3.6G 0 part [SWAP]
└─sda7 8:7 0 187.1G 0 part /home
sdb 8:16 0 2.7T 0 disk
└─sdb1 8:17 0 2.7T 0 part /media/4d98f9b3-512f-4d8b-96c6-4c6c4caaab40
sr0 11:0 1 1024M 0 rom
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sda is the main system drive and sdb is where I store lots of stuff, including the system backup.
Since this backup is from March 14th, I've made some configuration changes to some applications that I'd like to keep. They are all stored at /home so my question is, how do I restore the system without touching the /home partition?