Tried just revalidating the items by right click show errors and warnings rather than opening them?
This may possibly work although with Trainz you are never quite sure.
The last time I had a similar sort of problem, on a couple of signals, I closed CM searched for the kuid's in the local and original folders and deleted both copies from each folder and then ran a QDR, if you watch it in the window it should confirm the items have been removed, then just reinstall the originals, which you should then be able hopefully to fix and it should stick.