Yes, I went through the exact same thing. You do have to delete the MR 2012 Data Mart database and then set it up again. I was told this by MS Dynamics support. There are certain steps you need to go through though.......
Let me see if I can find them for you.....
If this error has been occurring for more than 3 days, then SQL no longer has a full record of all changes in Dynamics GP that need to be synchronized to the data mart database. Even if the issue has only occurred for a day, you can use the steps below to re-create the data mart. To fix the issue currently encountered, you will want to re-create the data mart database. To do this, use the steps below:
***All steps must be completed by a domain user assigned to the "Administrator" role in Management Reporter Security who is also a member of the local Administrators group on the server ***
a. Open the Management Reporter Configuration Console.
b. Click on the GP integration under ERP integrations
c. Click Disable Integration
d. Click Remove in the upper-right corner to get rid of the integration
e. Exit the Configuration Console
f. Open SQL Server Management Studio
g. Backup the Management Reporter database
h. Backup the data mart (usually DDM or ManagementReporterDM) database
i. Delete the data mart database
j. Open the Configuration Console
k. Stop the Management Reporter 2012 Process Service.
l. Stop the Management Reporter 2012 Application Service.
m. Start the Management Reporter 2012 Application Service.
n. Start the Management Reporter 2012 Process Service.
o. Go to File | Configure
p. Choose "Add Microsoft Dynamics GP Data Mart"
q. Follow the steps for the Dynamics GP provider at:
Microsoft Management Reporter: Installation, Migration, and Configuration Guides
www.microsoft.com/.../details.aspx;id=5916
r. When finished, be sure to click the "Enable Integration" button in the Configuration Console
s. Also be sure to fill out the "Notification Settings" section in the Configuration Console. This will send an email to the address entered when an issue occurs with the data mart. Without this populated, nobody will be aware of when an error happens with the data mart tasks and reports could possibly show incorrect balances.
If you do make changes to a Dynamics GP company in the future (such as creating a new company, or enabling AA for the first time), you can prevent the need for re-creating the data mart by opening the Configuration Console and clicking the "Reconfigure Change Tracking" option. I attached the CU9 GP provider guide for your reference.
Also note that Management Reporter 2012 CU10 may change some items as there are new features planned for how companies are integrated. More information on this is beyond the scope of this case, but will be released with CU10, due out in August/September 2014.