Zandronum

I have been attempting to create skins that are loadable in Complex Doom Invasion for private use, and I was doing so through directly modifying the three main files: complex-doom.v26a2.pk3, lca-v1.5.8_for_cdi_v2.2.pk3, and complex-doom-invasion_0.99.8e.pk3 (older versions, I know, but I prefer them over the new versions). My modifications are removing the line "Weapon.PreferredSkin" on every weapon and removing the +NOSKIN flag on the player class in each of the 3 files decorate scripts. I have also modified my skins file to apply to class "Doom Guy" which is the class name in Compex Doom Invasion.
So far I have been able to see the new skins with the proper sprite ONLY in the player options, and while I can select them and hear the custom sounds in game, they only display the default doomguy sprite in game, albeit with the scale from the selected skin (scale 0.5, scale 0.75, etc).
While I have been unable to get it working with these three files loaded, I have been able to get custom skins working if I only load the modified complex-doom.v26a2.pk3 file and lca-v1.5.8_for_cdi_v2.2.pk3, with removed Weapon.PreferredSkin and +NOSKIN flag, alongside the skins file applying to class "Doom Guy". With this I assume it must be complex-doom-invasion_0.99.8e.pk3, however after meticulously searching I couldn't for the life of me find out what it is making the skins appear as regular doomguy in game. I was wondering if it is an acs script doing it, however I have no expertise in acs whatsoever.

Unrelated to your problem but you should not modify existing files to achieve what you want. Make a patch where you set `+NOSKIN` on weapons.