Crowbar version:
0.51.0.0

Steps Taken:
Attempted to de-compile a model that seems to have $Body listed before $Model, while $Model has VTA flexes and eyeball definitons, to add eyes_updown and eyes_leftright flex controllers for eye movement support in Source FilmMaker.

Expected:
The model to de-compile and re-compile correctly.

Issues:
The previous $Body is now $Model, with the VTA flex definitions on it while completely missing the eyeball definitions. The previous $Model is now $Body, too, with no special parameters, and flexes not working. This means that flexes have completely stopped working.
I'm also not 100% sure whether the VTA file's flexes match up to the to-be-flexed mesh correctly, as Blender shows them to be wrong, but that might just be Blender linking VTA vertices incorrectly on import.

Operating System:
64-bit Windows 10

Samples:
https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=116797740 (Using Garry's Mod's own gmad.exe to turn it from a .gma file into loose folders and files, by dragging the .gma file from -/steamapps/common/GarrysMod/garrysmod/addons on top of -/steamapps/common/GarrysMod/bin/gmad.exe.)
According to Source FilmMaker's "change bodygroups" list (without de-compiling the model), the hands of this model come before the rest of the model, while it's the rest of the model that has flexes. Both parts were compiled as SMDs (and VTAs), not DMXes.
Also see this thread for slightly more information, I guess: https://steamhost.cn/steamcommunity_com/app/1840/discussions/0/1489992713708505122/



Irrelevant side-note: The "read this first" post's template has "Crowbar version:" with the bold code tags around it, though the rest of the lines are bold themselves without code tags around them. I'm guessing you set up [noparse] incorrectly there.