If you receive sep pay (JRTC) do you lose BAS as well?

By regulation, your unit should take BAS when meals have been provided. Most of them do not. What a lot of units do is if you file for family sep, they take the BAS. So you get paid 250 for family sep, but then they take 320 for BAS. It's not exactly the right way to do business, but most people wont blow the whistle if they will lose money.

The two are not mutually exclusive or inclusive. It is possible to get both separation pay AND has, or neither.

Yes, Command can do the paperwork to take away BAS when meals are provided, such as field training, training rotations, or even deployments. Usually they do not. BAS is NOT a family allowance, it is an individual Soldier allowance (which is why there is no "with dependents" rate).

Separation pay is an allowance for Soldiers who are separated from their family due to mission requirements for an extended period of time.

Most of the time, if you are gone long enough to draw sep pay, you are also in an environment where meals are provided, which is why the two often seem linked. But they are not actually.

I will refer you to have this conversation with your unit's leadership so IOT get the a full answer.