Are you 100% sure you’ve done nothing to the layer structure including naming and size?
BobLevine, yes, I'm absolutely sure. The first time I had this problem, I looked at the threads and found a solution that sorta helped me out as I was still adding layers in, and so now when I do these I create "placeholder" layers.
But with this particular graphic (and a few others), they've been complete as far as layers go for a few months. The only changes I've made have been small, like moving a portion of the line art.
The last time this happened was at home yesterday. The graphic file itself was unedited, but I had to relink it since it was my desktop rather than my work computer. THAT popped up as "the layers are different" blah blah blah.