I haven't Quite figured out the actual cause yet, but it's definitely a bug. Plus, in my opinion, it's Adobe's job to figure out the cause, not the consumer.
I have a sequence that has lots of clips and nested sequences. Some of them required some AfterEffects links. I think there are 3 different AE files being referenced.

Seemingly randomly, Premiere will tell me some, but not all, of the media is missing. If I save in premiere, close, then open again everything is found and fine. All of the after effects files are in the same location, and only a couple folders away from the premiere project file. So if one file is found, they All should be found. It's a bug.

Here's what I Think is happening, but have yet to confirm. I am guessing Premiere is assuming that all of the dynamic links are in the same AfterEffects project once you open one of them. I think this is only happening when I have Premiere and AE open at the same time.
In my case, one of the AE projects existed already and was imported into premiere. But then while that was open, a couple sequences were sent over to AE. As you probably know if you are reading this far, when you "Replace with AE composition" it sends it to whatever AE file is already open, or if none is open then it creates a brand new AE file.
My guess, is since Adobe is trying to do some path connections automatically, someone screwed it up and it doesn't work in cases that you have mixed methods of direct link, OR it just messes up occasionally if the premiere file is referencing multiple AE files.