How can i merge custom fields?
First create a Temp table with same structure and move all the data to the temp table. And then create a new column X and merge both the column A and B together and insert the values into the new column X

And once you are happy with the merge column X move the same against custom table matching with the entity ID - Job done 

Please refer to the below link for Example 
http://www.tutorialspoint.com/mysql/mysql-concat-function.htm