I'm having the same problem (playing as Scandinavia, Western tech group, own nearly all of several trade company regions, getting the same message), but when I go to the mod folder you mentioned, it's completely empty. I tried copying and pasting the regular technology.txt file into the folder, but still had the issue. The only thing I can think of that's different from ebs' situation is that I have Norse culture and religion, but that still doesn't explain why the mod folder is empty. Should I bug report this?
Edit: Actually, I figured it out. I had to go to my Crusader Kings folder instead of my EUIV folder, and I found the mod and the file under the eu4export folder. Now the companies are working fine.