Technically possible, though someone may have to write an application to do so. It does depend on what you want, however. Do you want scores added together, or merely the highest one chosen? Are there some cards that only appear in one scorefile?
I've actually a got a program that can do some of that, and I'll provide a link when I get home. If you're not comfortable using the command line, export your cards to two XML files, one for each scorefile and I can have a go at merging them. Might need to make some changes though, as it was also designed to merge definitions and categories and such...