The invalid textures had a few things in common. They did not update if I made a change in the substance factory, and when I opened the texture there was no image displayed. It did say it was invalid somewhere (after opening the file) but I do not remember where in the UI that message was located.
I found them by migrating different sections into a blank 4.27 project with the substance plugin activated and then attempted to open it in 5.2. (I always had to made sure that the substance plugin was still enabled if the opening in 5.2 was successful. There where a few false positives because of this.) I had a specific process to make it a bit more efficient, but I don’t know that it bears repeating here. Basically I did it by process of elimination. You could also look into using Unreal’s asset/data validation tools - I do not have any experience using these, but I imagine they are likely designed for scenarios like this.