Bottom Line Answer
Once you chapter is approved, the Separation Transfer Point (STP), will adjust your separation date to allow for the number of days of approved transition leave. If you are coming up on your ETS date and have already sold 60 days of leave during your career, then you may very well lose some of your accrued leave. Your other option is to take ordinary leave while waiting for the chapter to be decided.
In this case, you have to wait until the separation authority makes the decision on your conditional waiver. Much depends upon who the separation authority is and how quick it comes back. If it was referred for an Other Than Honorable, the chances of receiving an Honorable are slim. However, if you were referred for a General discharge, then the Brigade Level Commander is the separation authority and you may get the waiver.