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If they are going through the process of separation, the battalion commander must believe that there is at least some basis for a separation here, despite all the counter evidence.
The problem is that she hasn't been in the service long enough to be entitled to a board hearing. So, unless they are seeking an Other than Honorable discharge for her, she won't get to do a board hearing and the only people that will decide her fate will be the battalion and brigade commander. All she can do, in that situation, is submit a letter on her behalf, asking the next level commander to review it (an appeal), but that is as far as it goes.
She'd then have to try and correct the issue once she is out, through a DD Form 293 or DD Form 149 to the discharge upgrade board and military records corrections board, where a hearing would be permitted and where she could try to have the discharge status changed and her RE code adjusted to allow reentry (if that is her wish).
First, I didn't charge you anything. I am just a contractor, so I don't have anything to do with what is charged to you.
Second, you have not actually been charged yet. Your funds are on deposit and still belong to you until you choose to rate the service.
I am just now seeing your response because you didn't respond for so long.
Now, I can't tell you what they will do, just what they can do and yes, they can separate her due to the very short time she has the service. She isn't entitled a board hearing before separation, so the decision is entirely up to the brigade commander. The commander can certainly take into consideration the lack of evidence and retain her, but he doesn't have to and then her only recourse will be trying to correct the matter after she is out.