With regard to the APFT test the DA FORM 705 follows you when you PCS or move within units. In addition if you are in the ABCP the same applies. In addition both of these actions require a flag be initiated place per AR 600-8-2.
With that stated I see nothing wrong with the unit using your past APFT’s on the DA FORM 705. If they are looking at separating you from service then you can look at AR 635-200. Usually the regulations only requires the commander to initiate separation action but does not require the action to be approved by the approving authority. In other words the approving authority has the authority to allow you another chance in most cases.
If you desire to remain in service you might consider contacting JAG and a Senior NCO as ask them to assist you in preparing a letter to your Co and BN CDRs stating why you should be given another opportunity and why they will not regret providing you the opportunity.
In addition a separation action can be placed in suspension for up to two years. So the commander can process you for separation and suspend the action (much like an Article 15). If you do not perform to standard they can separate you pretty quickly.
Hopefully I answered your questions.
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