I have two mods, one adds a Quest, the other adds another Quest with a script that has a property to reference the first Quest. The first Quest's ID is 02002860, yet when I reload the two mods in the CK, the value set to the property mysteriously changes to 03002860 (the first byte gets altered to match the load order). The same happens in the game. I've checked the .esp file with a Hex editor and it conatins 02002860 both before and after the game. What's going on? Am I missing something?

As you've found, the first two digits (the first byte) represents the mod's place in the load order. There's no way to keep them the same unless you don't change your load order, ever.

The reason that it changed in the CK is because of the number of mods (esp/esm files) that you load when you edit the file.

So you're saying there is no way to reference objects in other mods, only master files?

http://www.gamesas.com/topic/1376413-skyrims-newest-beta-patch-the-ck/page__view__findpost__p__20831757

^ If you wanted to use something from another mod in your script.

Otherwise, yes, in order to use another mod's resources, you must have the other mod set as a master of your mod.

Talk about impecable timing . I'll just wait for the update then.