The database should be backed up using the in built act function, a standard backup utility won't do it as the ADF is constantly locked by the Act7 SQL instance (Unless it's disabled).
You can't "Compare" them as such, you would need to import the original master database into the new master database, if the duplicate checking criteria is correctly matching the duplicates it should create the missing records. Please see the following Sage KB article on merging databases.
Note: Backup your database before proceeding with this (File -> Backup -> Database).
http://kb.sagesoftwareonline.com/cgi-bin/sagesoftwareonline.cfg/php/enduser/std_adp.php?p_faqid=22042&p_sid=LbwlKT5k&p_lva=16623&p_accessibility=0&p_redirect=&p_sp=cF9zcmNoPTEmcF9zb3J0X2J5PSZwX2dyaWRzb3J0PSZwX3Jvd19jbnQ9ODU2LDg1NiZwX3Byb2RzPTAmcF9jYXRzPSZwX3B2PSZwX2N2PSZwX3NlYXJjaF90eXBlPWFuc3dlcnMuc2VhcmNoX25sJnBfcGFnZT0xJnBfc2VhcmNoX3RleHQ9SW1wb3J0aW5nIHJlbW90ZQ**&p_li=
