Have you used the CRA AutoFill option to import T4A? when you use Auto-Fill, it is really important to go through all the T-slips imported and make sure all the information is accurate with the original slip. It is one of the NETFILE conditions.
When a verification of the T4A is done after Auto-Fill, you'll have to open the T4A and select the source of the box 48. If you don't, the software won't be able to report this amount at the proper place in your return.
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