Just wire a FALSE to the advisory dialog input of "Open/Create/Replace file.vi". (Some higher level file I/O function do not expose this option, so you might have to use low level functions. You could also modify one of the high level function and save it under a new name. )
Alternatively, you could simply delete it before writing it again. The delete function is in the advanced file I/O palette.
How are you writing to the file?