However, if something gets messed up in the process (i.e. improper conversion of the files, something's not changed that should be [or vice versa], it gets some random extra trash bytes, etc), then they would be considered hacked [thus not tradable here]. Basically it should result in the same Pokemon as if you had used Bank. So unless you really trust yourself and the program, I wouldn't try it. Bank also doesn't allow some Pokemon through, so those Pokemon shouldn't be transferred either or would be "hacked".
There could be something else I'm missing, but that's what comes to mind right now haha.