New thought. You said two remote/TIU pairs. If the content of both remotes is not identical regarding locos and their IDs, you'll have a problem. I suggest pick the remote whose keys best reflect your wishes for layout, and back it up to your PC, using Loader 5.0. Then reset the other remote, which will clean out the data
Place one of the recalcitrant locos on an unpowered track. Using the reset empty remote, try a read. If no locos come up, try add engine. If either gives you an engine, edit the engine address to some ID number you've never used. Post results and we'll go on from there.
You said engine runs in conventional. If you cut power to the track, do sounds continue for more than 5 seconds or so? If not, bad supercap or battery, so engine can't hold an ID.