It is the usual frustration with the new knowledgebase why I posted in here because I couldn't find anything. After multiple searches, I finally found the answer:
How to correct out-of-balance issues in Payroll.
Before the Check Register has been updated:
Delete the out-of-balance entry, and reenter the employee's correct earnings information in the Payroll Data Entry window. Continue with normal payroll procedures.
Note: See Payroll Help for more information on Payroll data entry procedures.
If the out-of-balance issue still occurs after deleting and recreating the entry, perform the following:
Rebuild the following key files (see Related Article below How to Rebuild Key Files):
PR6 - P/R Payroll Data Entry File
PR8 - P/R Payroll Data Entry Tax Summary File
PR9 - P/R Check Printing Detail File
PRA - P/R Report Sort Temporary File
PR_42 - P/R Data Entry Tax Summary File II
Analyze and Relink PR7 - P/R Payroll Data Entry Line Detail File. (see Related Article below How to Analyze and Relink Line Files)