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be treated as "Violating rule".
-No because you filed B-2 extension before the B-2 I-94 expires.

If I withdaw my F application do I have to wait untill receving a "Withdrawed" notice before I can file another F application?
-Unless the B-2 extension is approved, no difference. If your B-2 extension is approved, and then F-1 is denied,  you can file another F-1 using the new B-2 I-94.
 
If I file a second F application before my first F application is actually withdrawed by USCIS, it is possible for USCIS to see two same I-539s there.
-It does not matter.

Will this leads to another "Violating rule" 
-No if the B-2 is approved.

Please help！