Are you sure you choose "Wallet with two-factor authentication" rather than "Standard wallet" when you attempt to restore access to your wallet/bitcoin?
This makes no difference. Even if you select "Standard wallet", Electrum will still recognize the seed phrase as 2FA and will continue with the restore process as such, and still offer you the chance to keep or disable the 2FA authentication.
Depending on the age of your wallet what also might be happening is that your wallet doesn't support native segwit.
As he is restoring an Electrum seed phrase with Electrum, then this is not a concern.
OP, when you are restoring from the seed phrase(s) and you get to the page on Electrum in which you type in the seed phrase, after you have typed it in some text will pop up saying "Seed Type: xxx", with xxx saying 2FA, Segwit, Legacy, or something similar. What does it say for both your seed phrases?
When you restore the two seed phrases, what letter do the addresses in both of them start with? Do you recognize the addresses? If you put the first few addresses in to a block explorer such as blockchair.com, do you see any transactions or balance?