We can close this issue, I have solved my own problem
I created my own extension agi in extensions.conf under globals.
[mainmenu]
exten => 0094*00000,1,agi(selintra,Inbound,${EXTEN})
(Number hidden to protect the guilty)
It's the same as the entry that doesn't work, but has the required * in the number
This way it appears to stay in place after a commit and I know have incoming calls working again on both my username/number and more importantly on my DiD.