The best way I think to do this is after you have made your changes to Database A, run a SQL Compare between Database A and an empty database. You will obtain a synchronisation SQL script which you can extract and process - you can run through this script extracting all the lines containing 'sp_addextendedproperty' and insert them to another SQL script (you could write a simple VB application to do this for instance, or use a Perl command). This SQL script in SSMS would then write the extended properties onto Database A for you.
Running SQL Compare then between Database A and Database B would obtain another SQL script that you could process in a similar way, and run that against Database B, and synchronise them.
The alternative would be to write a Toolkit application, extracting and running only the lines containing 'sp_addextendedproperty'