I recently updated my CC to the latest version and then opened a project I've been working on for the past month. All the After Effects linked comps show like vertical color bars in the project. I have tried to relink them but that only messed up the few comps that were still showing up as normal.
You have to update everything.
As Rick says, it looks like you didn't update all of your software.
What version of Premiere did you have before?
What version of AE did you have before?
What version of Premiere do you have now?
What version of AE do you have now?
Exact version numbers down to the last decimal, please.
In the future, I'd suggest NOT updating in the middle of important projects.