I'm not sure about the usage of "in" and "after". For example, it's January now and I got rejected in a job application, some one tells me that I can re-apply in six month. Is this "in" the same as "within"? Does it mean I can re-apply in the period between January and June but not after June? Or does it mean I should re-apply after June?
In this case, you can re-apply in six months means you must wait until six months after your first application to file a new one (i.e. June).
If they intended to say that six months was the latest you could re-apply, they would have said you can re-apply for six months or you can re-apply within six months. You could also communicate this sense by saying you can re-apply in the next six months.