The 5th day we went to MK. Stopped by inside Guest Services again and found out that only 1 day had been deducted from the special 4 day tickets, the rest came off the other set of tickets. Again, they said they 'fixed' them and we thought all was well.
Feeling paranoid

I decided to confirm all was well and checked our MDE accounts and noticed things weren't jiving as to usage. I contacted WDW's ticket research department for assistance. Had to fax them front & back of all tickets and our drivers licenses. They called me back and said things were so messed up at that point that they would just issue a new set of re-assignable tickets to replace the original set and link them to our MDE accounts. Yea!!! but glad I remembered to check right away.
What a total hassle.
The NE tickets seem to be causing problems when they are linked to an account that also has another type of ticket, such as an AP, a special 4 day, or an expiring MYW.
Disney's official reason for discontinuing the NE ticket option was that those tickets caused so much confusion. It seems to me it is not the NE tickets themselves that are causing the confusion, but rather the way they are handled by the fairly new MDE application. Basically MDE seems to be confused on which ticket to use. Currently the only "fix" is to have guest services prioritize your tickets, and hope they do it correctly. (That seemed to work for quirty30 in post 9.)
I am disappointed that rather than spend programing dollars to improve MDE, either by letting guests prioritize their own tickets in their MDE profile, or improving the deactivate function so that actually did what it implies (see post #1), instead Disney just decided to eliminate NE tickets. Problem solved. (at least after all the existing NE tickets have been used)
However, for those of us who still have those old NE tickets, if we link those NE tickets to a profile that has, or will have, other types of tickets in it, we are at the mercy of Guest Services to properly prioritize our tickets. I assume we will have to go back to Guest services every time we add a new ticket to our profile to make sure our tickets are still prioritized the way we want. Again what a total hassle.
Here is my solution:
I plan on setting up a second profile for myself on MDE and only linking NE tickets to that profile. I would link any expiring tickets, including AP's to my original profile. Then, when I linked a future room reservation to my second profile, I would get a magic band that would only have access to my NE tickets. However, for trips where I linked my room reservation to my original profile, I would get a different magic band that would only have access to the expiring tickets linked to my original profile. That way I can have total control over which ticket gets used, and make sure my NE tickets are never used accidently.