It is never the proper route to backdate payroll (whatever that means).  If you are suggesting that late payroll returns be filed, with payment of penalties that then with some work might be abated when neither you nor IRS has time to deal with them, what is the tax consequence of not doing so?  The SE tax she is paying equals (more or less) the FICA tax she would owe.  If she is paying her 1040 income tax quarterly, the FIT withholding that might have been owed on the 941s is collected anyway.

2024 is water under the bridge.  No harm, no foul.  Get her into compliance for 2025.  And as for what the previous CPA said:  That might be what was suggested, and she didn't want to do it, is why she came to you.  

My first reading of your post led me to think that the corporation's customer was issuing a 1099 to her personally for work done by the corporation.  Now, I wonder if you mean the only 1099 being issued is the one that her corporation issues to her.  In either case, it hasn't seemed to bother IRS yet.  And if it does, you may still have 2023 to deal with.