Ok, first of all Raptor thanks for the help; it was really something that I could never have come up with by myself. So, this is what happened when I followed your instructions and used Mission Commander. I did exactly like you said and the skins didn’t change at first. BUT when I used the “Change Skin " button on the loadout page the skin changed to the correct one in both the loadout page and in the 3D word while flying. So I am assuming that your solution requires that I edit each TE with Mission Commander first and then change the skin in the loadout page, which is quite easy and simple actually.
However I am confused about something that I read in the camo.cfg file in the Ikaros Theater, where it says the following:
_” Camouflage override feature. Now is possible to override default texture set computation and specify exact texture set for sqadron via txt cfg file called camo.cfg in campaingn/save folder (each theter can have its own)
Format of camo.cfg:
First line is number of specified sqadrons (max 256). Add 1 on the total for each line you write below it.
Then each sqaudron is defined on 1 line by 3 numbers.
First number is Team ID. For Ikaros Theater 1 is Greece, 2 is Turkey, etc. Check Mission Commander for the rest numbers / countries ID’s.
Second number is Squadron Name. This must be a number, most likely the real Squadron number.
Third number is the desired texture Skin Set for the Squadron. Check the corresponding 3D model on LodEditor to determine and arrange the Skin Sets as appropriate.
Note: Skin Sets is counted from 0."_
The way I understood all that was that if I changed the skinset number for these aircraft in the camo.cfg file from 0 (default value) to 5 (which seems to be the correct skinset from MC) I would get the correct skins in the game for all TEs and campaigns regardless of any additional processing with MC or any other software. This apparently has not been the case, so was I wrong in my original understanding of the quote in camo.cfg, and if yes, what does that quote really mean ? Anyway, you already provided me with a more that adequate solution to my problem which seems to be working perfectly, so my interest in this is now simply out of curiosity. Anyway, once again thank you for your answer and keep up the great work with this amazing theater that has so much more to offer ( I would really love to see some HAF A-7s someday in the future and I can only hope for a cockpit for the A-7 too :D, but I guess the devs know best and I have absolute confidence in them).