I changed the flags as I did in AoE III thanks to Resource Manager , but I can’t make Malta (or Knights of St John or Morgan Black) playable . I opened civs.xml with “notepad”, but I can’t find the name faction and / or where to change from 0 to 1.
When I make Malta playable, I will put the flag of Italy (which I found)  in its place and change the name of Malta to Italy .
Check the civs.xml
The civs have a number somewhere wich defines what kind of civ they are.
"It’s more or less like this:
0 = European
1 = Native
2 = SPC Native
3 = Asian
4 = SPC Asian
5 = SPC European
The game code has separate checks for SPC civilizations, since they don’t share all features from their playable counterparts. So, instead of leaving them as hardcoded, I assigned separate civtype IDs for them" - thank you [redacted] for this information