Running 2015.3 and got the dreaded error along with Genarts Sapphire errors for every single plugin. Fun.
I have 2 machines (Home and Office) that are licensed and identical software setups and sync projects through a portable hard drive. I also image each machine and incrementally update. After rolling back my home machine for whatever reason to an earlier drive image I noticed this error popping up and went down the rabbit hole of trying to find out why. Lots of info out there for all sorts of problems.
FIX: (for my situation) was simply to run the Premiere project to allow the files to transcode audio again. Then open After effects and then Media encoder. This got rid of the errors.
What confused me is that all my caches and database info are on separate SSD drives and aren't impacted by OS drive restorations.
3770k, 32GB RAM, GTX 1070 8GB, W7x64
thanks for sharing the problem and the fix. I am not using Sapphire plugins but just making sure you did not overlook these trivial steps: is your Ae version the updated one 13.8.1? is your Sapphire plugin updated to the latest release: Updates | Sapphire Plug-ins | After Effects | GenArts ? does this error appear in 13.7? have you tried getting support from the sapphire forum?
The problem wasn't caused by Genarts plugins, but did affect them if they were part of the project. I verified this.
Again, the solution was to merely run Premiere and allow the files to render preview files over and the errors were gone. Whatever versions were the latest at the time of my original posting were what I was using as I checked for the latest versions on everything.