I'm not understanding the way you're describing the situation.
You say, "When I RE-apply master A to master B, primary text flow on master B is gone."
What are you actually doing? You don't reapply a master to another master. You apply a master to the document pages. Or, you apply a different master to the document pages.
Try to explain more clearly, or post a screen capture.
I'm RE-applying master A to master B. I just want to "reset" master B. I'm doing that by drag'n'drop master A onto masterB.
I think I describe my problem clear. One master is based on another master (you know that this is possible?).
My problem arrives when I applying master A one more time to reset any changes on master B
I think the problem may be in your workflow. I work a lot with master pages, and I've never tried to "reset" a child master by dropping master A on master B.
Why do you want to "reset" master B? What do you want to change on master B? Please be more explicit what it is you want to change. I think screen captures would help. You can use the camera icon in the edit box to attach a screen capture.
Steve is right , it seems the document specific and workflow related issue ,
you have Master A applied on Master B then there is no need to re-apply it , changes in the Master A will be automatically updated in the Master B.
BTW if you create a fresh new master page C and apply the Master A then does it work ?
, also what if you apply the None Master first on the Master B and then apply the Master A , does this work ?