Have you tried to open after effects and save the project agian using "Save as". I had a similar problem when elements were missing and did not update correctly.
It is just a shoot in the dark, but I hope it was to some help.
Have you tried re-linking the AE comp just like you would footage? That has worked for me, although I have only had this happen rarely. I also do the "render and replace" thing because I have run into issues at render where the linked comp hasn't shown up even though it shows fine on the timeline. I assume the Illustrator file shows up fine in AE.
One thing I have noticed is that it seems to unlink the illustrator files from the live text template when I export via media encoder, but if I export straight from Premiere it generally comes out ok.
I have had a certain amount of success closing it and re-opening it, re-saving it etc. Not sure that I can re-link these text templates because premiere doesn't think they're unlinked - it's just that the Illustrator file that is a part of the AE comp has got unlinked somehow. And yes brian704 the illustrator file is showing up fine in AE.
If Premiere doesn't think they are unlinked just do a "file replace" and re-select the AE comp. I have had to do that on occasion. It is also necessary when you need to use a different version of the comp.
Are you still experiencing this issue, Tristan M? Please let us know if you still need help with this issue.
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Be aware that today's update to Premiere Pro and After Effects bring a whole new (better) way of doing this.