Don't know where you get the idea that you have to wait for the 90 days to be up before being activated on the new dongle. The only thing the 90 days refers to is that to keep TLC coverage going you have to let the iLok site see your dongle every 90 days which can be done on any computer with the ILM s/w. Has nothing to do with licenses being voided.
This was my take-away as well. Everything on their website indicates that a new dongle requires brand new ZDT+TLC, which - by definition - necessitates a new 90-day refresh period be instantiated. It doesn't make any sense that a new dongle would be subject to an old, voided dongle's 90 day cycle.
There's nothing on the iLok site that a new dongle requires brand new ZDT/TLC. ZDT/TLC is completely optional for one's ilok. The new iLok is NOT subject to any old 90 day cycle. You may be confused in that each iLok has to have it's own ZDT (if you want it to). You don't have to have ZDT on a new/replacement iLok. An old iLok's ZDT does not carry over to a new iLok. Each iLok is a separate entity.For Instance I have two iLoks. Each has their own ZDT setup. I don't have to have ZDT on the second iLok but I choose to be safe and have both covered. That way if I have an iLok that seems to be flaky I can move the licenses over to the other one with no problem.
I've been dealing with iLoks for almost a decade now and know what's what.