I believe you have specified a file operation type of "create" when using Open/Create/Replace File".
When I try to write to a file that already exists in this mode, then I get the two dialog boxes you mention:
Dialog Message A - " This file already exists Do you want to replace it?"
Dialog Message B - "File exists"
You could do a couple of things to circumvent this:
1 - Replace the "create" mode going into the "Open/Create/Replace File" with a mode of "create or replace". Now, you will only get one dialog that says "Replace existing ?"
2 - If you open up the "Open/Create/Replace File" VI, you'll notice that it contains the function "File Dialog". "File Dialog" is responsible for generating Dialog Message A as mentioned above. There's nothing you can do about this dialog programmatically except change the mode of the operation ("create" vs. "create or replace").
3 - If you further investigate the block diagram of the "Open/Create/Replace File" VI, you'll also notice that it generates a dialog box that corresponds to Dialog Message B mentioned above. One option for you is to save a copy of the "Open/Create/Replace File" VI and modify this copy--eliminating this extraneous dialog message.
Personally, just changing the mode to "create or replace" seems easiest.
Please see the Word document I've attached which shows screenshots and explanations.
-SciAuto