My Desert Combat mod still seemed to work fine after I got V1.3 all working properly. But there is also a new update patch for Desert Combat, to fix other issues they had (graphics changes in V1.3). So go and download that.
The DC mod is a standalone mod, so just sits in a folder until you choose to activate it. It won't/shouldn't affect anything about BF1942 or the RTR mod.
Yeah DC 0.25c works with 1.3, however that "custom mods" button seemed to have disappeared in the main menu now. :(
What you mean dissapear. Reinstall.