So currently after one of my mods updated my engram are at -3262 points. While it is unlocking the normal ark engrams each level the modded stuff such as s+ and other things are not unlocking how do I fix this?

Would recommend two things:

1) Roll back to your latest backup before the update caused an issue. 2) See if that backup is as corrupt.

If yes, you'll have to play "Whack-A-Mod" to see what broke.

Step 1) Disable all the mods. Step 2) Reboot. Step 3) Restore the last backup and see if the backup is good. Step 4) Re-enable one mod. Step 5) Reboot. Step 6) See if the game is good, if it is proceed to step 7, if not you have found the bad mod. You'll need to seek assistance with that mod's creator. Step 7) Repeat steps 4,5 and 6 until they're all re-enabled or you find your bad mod.

If no, then you might have to just move forward with the last backup as something may have just "ARKed." on the last update.