After degrading the live beta site back to J 3.8 the EFL is working, as mentioned I did a test on local sever again installed the j38 site and did another upgrade to J39 this time the EFL module is intact.
I’ve gone ahead and upgraded the live beta site for the second time to J3.9 and AFL appears to be working, no errors
I cannot explain why I had the error on first attempt, possible ba bad upgrade but you know more about this than I, hopefully you find some answers.