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My initial testing shows that basic mech modifications are working for mechs included in the base game, but not DLC mechs. Could that be the issue you're seeing here?
 
yep, and modtek as we know it is hosed which actually yea that's not a problem as long as the rest of the things work..
My own Sandman mech I reworked to just use the rifleman model and it shows up in the skirmish mech lab, and game mech lab but when I launch a mission with it.... No mech.

I knew there would have to be a patch on the patch. Going to have to wait for it.

(BUT DADDY MITCH I WANT IT NOW! *rants, screams, throws things*)

And it's even worse.. Been trying to create a mech model asset to use in game with the top half of a rifleman and bottom half of a shadowhawk.. been making "poor" progress, and now its come to a total screaming halt.

Fixed it so that mods don't break save games but may have missed the part where fixing that broke mods.