I am also a little confused on this one. When you say "base rules" do you mean you are setting the baseRules for all the xml databases to true for Martial Law or that you are just setting Martial Law to use=true? If you are setting all xml databases under martial law and college of magics to baseRules=true then yes you will get a conflict and I would be surprised to hear if the app would be stable.
Changing the database settings is certainly encouraged, but it must be done with prudence and knowing what that change means to its communication in the software. Baserules only apply to those xml database you want to be the base rule in the software. You can't have the same xml database in Martial Law and in College of Magics both be true for baseRules. Only one xml database can be set to baseRules true. Here's a clearer example.
Harp Fantasy, Martial Law and College of Magics all have the same xml database structure. For example a profession database exists for Harp Fantasy, Martial Law and College of Magics regardless if there is no information from the book to provide. I but the database in there on the off chance the user wants to add something of their own. In the case of the profession database only one profession database can be set to baseRules=true, be that the profession database in Martial Law, College of Magics or Harp Fantasy. If you set one of these databases to baseRules=true one needs to make sure there are base rules defined. I admit, it's not a perfect system, and it can be improved, but this should be enough to help in making sure the databases talk well to the application. If you have any further questions, I will be happy to fill in the blanks. This part of the application I have noticed is the trickiest part. So I do plan to look into ways to improve it, but for now, it is where it is.
The best way to know if you have the baserules defined correctly is to make sure you have only set database set to true between all the other databases. I believe there are 17 database files per database installed. Therefore in the whole config.xml file, there should be only 17 databases set to baseRules=true. The rest should be set to false.
