Can I substitute the BN letter of recommendation for a BDE commander LOR?

I was in a Logistical Support Battalion. We had an unusual make up, and did not actually have a HHC component. I tried to have the XO write the Company LOR and had the BN CO write his LOR. I had the packet rejected because I did not have an actual company CO LOR. That was the first in a string of odd reasons for subsequent denials from my proponent to push the packet up. I eventually got tired of the problems.

Anyway, I assume you are in a HHC of a brigade and do not have a BN co (no Battalion). I would be in the same boat if I tried today because I also do not have a Battalion within my unit structure.
I suggest the BDE include a statement indicating that he is writing the letter in lieu of the BN commander due to the organizational structure of your unit (If that is the reason)

If you fall under a BDE headquarters rather than a BN headquarters this would be fine. If not, it's best to go with the BN commanders LOR.

No, you can always add more, but never less than the required documents. Not being able to produce an LOR for the appropriate level of command sends a clear signal to the board that the people who work the most closely to you aren't willing to recommend you.