Sorry this is so late, but I just had the same problem and while looking for an answer, I found this link.
I tried several of these suggestions and found a combination that worked for me.
It seems that when I deleted some midi content at the end of a clip, then moved the end marker on the clip to shorten it, some midi data stayed on the track but didn't show up in the Event List.
I used the Ctrl-End suggestion and it showed the end of the clip including the "phantom" data. I put that point in the end selection, then put my proposed end in the beginning selection, then did a Delete Special and clicked all the boxes. That deleted all the phantom data and the project end is now where it should be.
I hope someone can use this.
