How can I delete a certificate that got restored from a backup under iOS 10/11?
I found a certificate in my iOS device's Certificate Trust Settings. And it was not be found in Profiles. Finally I remove it by add the cert file again, and then I can found and remove it in Profiles. 

At first, I can't found the cert file, because this CA was installed years ago. So I did these things:


Backup iPhone to Mac, View backup file by some software (I used iMazing)
Find TrustStore.sqlite3 in Backup/KeychainDomain/ and export it to HOME DIR.
Use this project https://github.com/ADVTOOLS/ADVTrustStore to export certfile

./iosCertTrustManager.py -t ~/TrustStore.sqlite3 -e ~/foo.crt

Airdrop or Email this crt file to iOS device, and install it.
Find it in Settings > General > Profiles and Remove it. 
It disappear in "Certificate Trust Settings"


Done.