In the VISUAL STUDIO 2015 there is a comparing of SQL databases.
Branches of the register can be compared by means of Beynd Compare, etc.
These tools do not allow to compare files of export of *.cex vaults, but can be the useful.
Possible exists utilities for file comparison of 2 files *.cex (I dont know) - but everything depends on the fact that it is necessary to compare - in these files only a part of settings.
It is also possible to keep results of quiries to the necessary tables in SQL Server Management Studio, and then to compare them.
If it is very necessary - it is possible to create on the basis of quiries of SQL *.crp files, for use in the Reports Generator PDM, and then to compare the results (but hardly it is almost expedient - my personal opinion).