This is a normal process. You are upgrading from an older version and it has to create indexes. Run the sanitize DB routine first.
After upgrading from "4x, 5x or 6x" versions of Add2Exchange to the latest release, you should run this test. This test will solve a particular kind of issue where items don’t replicate to one (or more than one) user in the Add2Exchange Event Log, there are errors about "transaction rollbacks".
http://support.diditbetter.com/kb/A2E_183.aspx - This also solves the case of creating indexes. For these older version upgrades, you must first upgrade to the latest edition of Add2Exchange and then before (or if it doesn't open) opening up the Add2Exchange Console, run this procedure above.
[FROM HERE: http://support.diditbetter.com/kb/a2e_219.aspx]
AND then open the A2E Console again. It should open.
IF you have any bad rows in the database, before the next synchronization, edit each relationship once in the A2E Console so that "destination item deleted" is set to recopy. Then after a full sync, you can change it back. If you wish, we can do it as per an incident and recertify your box http://support.diditbetter.com/premium-support.aspx
Hope this helps