This happens because when generating the electronic certificates in the company with the same PAYE number, the same certificate number (eg 0000001) was used when generating the file. So when you import the file, E@file identifies that you have this certificate number already and then overrides the one that was imported from the first file, now all of the certificates and their values aren't in the E@syfile system and the EMP501 only shows the values from the certificates in the system.

Unfortunately this is something that happens quite often, and it is complicated and time consuming fix.  Due to this, I truly advise that you ready get a consultant to assist you in rectifying this matter - especially if you have a lot of exceptions and employees terminated prior to 1 September.  To make a booking, please visit our website

Once you have generated your Electronic certificates in Year End, then the system will allocate the first certificate number that you use to the masterfile and this number can not be changed no matter how many times you try to recreate the file with different numbers.

There is two ways that this can be fixed:

Option 1:

Completely disregard your current Copy Company, restore back to February and redo the Year End process and Copy Company from scratch.  Believe it or not, this is the option that requires the least amount of effort.  The cons to this Option is that you might struggle to restore your backup, and if you have renamed the live company once you have rolled over, you will need to manually restore your February company and this might cause your employee count to be reached.  If you have 2 companies, the below steps only need to be done in one of the companies, if you have 3, then it will have to be done in 2 and one of the companies can be left in the original state

If you didn't rename your company after rolling into the new year.

1. Make a backup of your live company
2. Restore your February backup
3. Redo the Year End and Create a New Copy Company
4. In your New Copy Company, Clear all the exceptions
5. Then generate your Electronic certificates with a completely unique New first certificate number (Eg. 31000001, 98700001, 56800001)
6. After you have created your New Copy Company, you can restore the Live company backup that you created in step 1
7. In E@syfile you will have to Delete all the files that you have imported for this period (Utilities, Delete Import Payroll File log)
8. After the import file was deleted, you will then re-import the files (All the files and not just the one that you restored for)

If you did rename your company after rolling into the new year:

1. You will have to manually extract the previous years February company
2. Redo the Year End and Create a New Copy Company
3. In your New Copy Company, Clear all the exceptions
4. Then generate your Electronic certificates with a completely Unique New first certificate number (Eg. 31000001, 98700001, 56800001)
5. In E@syfile you will have to Delete all the files that you have imported for this period (Utilities, Delete Import Payroll File log)
6. After the import file was deleted, you will then re-import the files (All the files and not just the one that you restored for)
7. After the file balances, I strongly advise that you delete the previous years company that we manually restored (File, Delete) and refresh your registration to fix your employee count.

Option 2:

Option 2 doesn't involve restoring any backups, and can be an easy option if you don't have any terminated employees (prior to 1 September).  However, if you have employees terminated prior to 1 September, then this option becomes rather strenuous, and I would once again want to advise you book a consultation for this.

Before I get started, you are probably wondering how would you identify if you have employees that have been terminated between 1 March 2018 and 1 September 2018.  You can pull the terminations report (View, Payroll Reports, Appointments and Terminations, Terminations).

I don't have any terminated employees at all in both of the companies:

1. Choose one of your companies and open it's Year End Copy Company
2. Click on Utility, Clear Utilities, Clear Certificate Numbers (if you do not have a Clear Utilities option under utility, you are either not on 2020 Update 1a or later, or if you are on this update you have not run a legislative release)
3. The system will bring up the below prompt, it is imperative that you only click on Yes if you DO NOT HAVE TERMINATED EMPLOYEES PRIOR TO 1 SEPTEMBER:
4. It will then ask you if you want to make a backup at this point, I strongly recommend that you make a backup, once clicking yes please continue with the backup process as per usual.
5. It will then tell you that your certificate numbers have been cleared.
6. Run the exception report  and then generate your Electronic certificates with a completely Unique New first certificate number (Eg. 31000001, 98700001, 56800001 etc.)
7. In E@syfile you will have to Delete all the files that you have imported for this period (Utilities, Delete Import Payroll File log)
8. After the import file was deleted, you will then re-import the files (All the files and not just the one that you did a clear certificate numbers for)

I have terminated employees in the one company, but none in the other company:

1. Open up the copy company where there are no terminated employees
2. Click on Utility, Clear Utilities, Clear Certificate Numbers (if you do not have a Clear Utilities option under utility, you are either not on 2020 Update 1a or later, or if you are on this update you have not run a legislative release)
3. The system will bring up a prompt asking if you are sure, it is imperative that you only click on Yes if you DO NOT HAVE TERMINATED EMPLOYEES PRIOR TO 1 SEPTEMBER.
4. It will then ask you if you want to make a backup at this point, I strongly recommend that you make a backup, once clicking yes please continue with the backup process as per usual.
5. It will then tell you that your certificate numbers have been cleared.
6. Run the exception report  and then generate your Electronic certificates with a completely Unique New first certificate number (Eg. 31000001, 98700001, 56800001 etc.)
7. In E@syfile you will have to Delete all the files that you have imported for this period (Utilities, Delete Import Payroll File log)
8. After the import file was deleted, you will then re-import the files (All the files and not just the one that you did a clear certificate numbers for)

I have employees that was terminated before 1 September in both of my Companies:

1. Open the copy company that has the least amount of employees that where terminated before 1 September
2. You will now have to go to each of these terminated employees Tax tabs of their Edit, Employee Masterfile screens and make a note of the employees Tax Certificate number (See below example)
   1. John Brown, Tax certificate number '0000009' and termination date 30 June 2018
   2. Sally Smith, Tax certificate number '1000015' and termination date 31 March 2018
3. The system will bring up a prompt asking if you are sure, you will now click on yes, because you have made a note of all the terminated employees before 1 Septembers employees tax certificate numbers. 
4. It will then ask you if you want to make a backup at this point, I strongly recommend that you make a backup, once clicking yes please continue with the backup process as per usual.
5. It will then tell you that your certificate numbers have been cleared.
6. Run the Exception report to ensure that there are no exceptions
7. You will now have to re-allocated your terminated employees certificate numbers one by one so it will match what the certificate number was in the Bi-Annual submission when SARS received their Final Certificate:
   1. Navigate to View, Statutory reports, IRP5/IT3a electronic certificates
   2. Filter for only the first employee you made a note of (eg. John Brown) and click on ok
   3. Enter the first certificate number as the one you made a note of (eg. 0000009) and generate the file
   4. You will now see if you check his masterfile that his certificate number will now display as it was before.
   5. Now you will move on the the next employee (Now only filter for Sally Smith and make her certificate number 1000015) and generate the file until you have done so for all of the employees terminated before 1 September.
8. After you have re-assigned all of the terminated employees certificate numbers, you will have to generate the Electronic certificates again, this time for all employees (Including all the employees you manually assigned certificate numbers too) and you will use a Unique Certificate number (eg. 50000001, 25000001, 2050001 etc)
9. In E@syfile you will have to Delete all the files that you have imported for this period (Utilities, Delete Import Payroll File log)
10. After the import file was deleted, you will then re-import the files (All the files and not just the one that you did a clear certificate numbers for)

As I said in the beginning of this article, this can be a very confusing, time consuming and challenging exercise.  I still highly advise that you have a consultant to assist you with this, if how ever you are confident in doing this on your own, I advise that you make a backup before getting started - just for in case.