Can a med board overide a chapter 9 or a chapter 13?

Please see AR 635-200

"1–33. Disposition through medical channels
a. Except in separation actions under chapter 10 and as provided in para 1–34b, disposition through medical channels takes precedence over administrative separation processing.
b. When the medical treatment facility (MTF) commander or attending medical officer determines that a soldier being processed for administrative separation under chapters 7 (see sec IV), 14, or 15, does not meet the medical
fitness standards for retention (see AR 40–501, chap 3), he/she will refer the soldier to a Medical Evaluation Board (MEB) in accordance with AR 40–400. The administrative separation proceedings will continue, but final action by the separation authority will not be taken, pending the results of MEB.
(1) If the MEB findings indicate that referral of the case to a physical evaluation board (PEB) is warranted for disability processing under the provisions of AR 635–40, the MTF commander will furnish copies of the approved MEB proceedings to the soldier’s GCMCA and unit commander. The GCMCA may direct, in writing, that the soldier be processed through the physical disability system when action under the UCMJ has not been initiated, and one of the following has been determined:
(a) The soldier’s medical condition is the direct or substantial contributing cause of the conduct that led to the recommendation for administrative elimination.
(b) Other circumstances of the individual case warrant disability processing instead of further processing for administrative separation.
(2) The authority of the GCMCA to determine whether a case is to be processed through medical disability channels or under administrative separation provisions will not be delegated.
(3) The GCMCA’s signed decision to process a soldier through the physical disability system will be transmitted to the MTF commander as authority for referral of the case to a PEB.
(a) Copies of the GCMCA’s decision will be furnished to the unit commander and included in the administrative separation proceedings.
(b) The unit commander will suspend processing of the administrative separation action pending the PEB.
1. If the soldier is found physically fit, the administrative separation action will be resumed.
2. If the soldier is found physically unfit, the administrative separation action will be abated.
c. Disability processing is inappropriate if the conditions in b(1)(a) and (b) do not apply, if UCMJ action has been initiated, or if the soldier has been medically diagnosed as drug dependent. (See para 14–12c.) Accordingly, disability processing is inappropriate in separation actions under chapter 10."

If the chapter proceedings have already been started, it would be rare for a Med board to step in.

It is very very rare to do that. If the medical issue came from any actions on your own then it won't. If you are facing separation under chapter 9 or 13 then you will most likely have to deal with that and hope to try to get something from the VA. But the nature of the disability is going to be called into question.