I've got an interesting issue myself...
Using Morghs (on WB 1.174) to tweak the Prophesy of Pendor mod, and after a recent patch that overwrote the troops.txt file, I expected to have to go into Morghs and re-do the tweaks I had made. But in Morghs, they were showing as still being there. But when I open the troops.txt file itself, the values/changes don't match, and don't reflect in-game.
I presumed that Morghs would read the .txt files each time it ran, so I tried what I thought would be the nuclear option...delete everything, re-download, and use fresh files (both Morghs and the mod). But even with removing Morghs completely, it still shows the last changes I tweaked to the Troops file (and partytemplates.txt as well!).
Not sure how this is even possible..but it is frustrating as heck.
Update: After a lot of trial-and-error, the only thing I can think of causing it somehow (compared to previously) is a recent upgrade to using Windows 10.