I just did the same process with DB Connect v2. I was migrating from DB Connect v1 (DBX) to the new app but already had 50K+ rows in Splunk.
From the Splunk docs here's the particular line:
A checkpoint value: The checkpoint value is how DB Connect determines what rows are new from one input execution to the next. The first time the input is run, DB Connect will only select those rows that contain a higher value in the checkpoint column than the checkpoint value you specify. Each time the input is finished running, DB Connect updates the input's checkpoint value with the value in the last row of the checkpoint column.
http://docs.splunk.com/Documentation/DBX/2.3.1/DeployDBX/Createandmanagedatabaseinputs
So in my case, I entered the highest value that Splunk already had indexed after I turned off the DB Connect v1 plugin.
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