I found out my brother who was helping me didn't re-plug back into the damper sensor, which caused the chassis error. However, I also ended up making an adjustable height sensor arm myself. Attached a pic of the parts I used incase anyone wanted to make their own.
Once you get the warning it doesn't matter what the battery charge state level is. You'll have to get the dealer to reset it and hopefully they know what they are doing.
Damn...Thanks for letting me know. They already ordered the BMW battery, so I'll talk them next week. I'm hoping is just a lack of understanding because its a BMW system and not a bigger issue.
The dealership did some research and told me that because they replaced it with the Toyota Branded battery (00544-H9AGM-T50) it will continue to throw the 'Replace Battery' warning. So they now need to order the BMW branded battery that has a "barcode" on it.
For those who had their battery...
I just had the dealer replace the battery and re-register it, but after 10 minutes of driving home the "Replace Battery' warning came back on. Would anyone have any insight to why its still throwing the warning?