I was able to re-run Convert-SPWebApplication on the web app. However, I first had to remove the trusted identity token issuer and trusted root authority:
Remove-SPTrustedIdentityTokenIssuer -Identity "ADFS"
Remove-SPTrustedRootAuthority -Identity "ADFS Token Signing Cert Parent"
and then re-add it.
Next, I ran Convert-SPWebApplication using a database switch to point to the specific database:
$wa = Get-SPWebApplication -Identity "https://web.app.url"
$tp= Get-SPTrustedIdentityTokenIssuer "ADFS"
$skipList = "D:\ADFS\SkipList.csv"
$database = Get-SPContentDatabase -Identity "Content Database Name"
Convert-SPWebApplication -id $wa -To CLAIMS-TRUSTED-DEFAULT -From CLAIMS-WINDOWS -database $database -TrustedProvider $tp -SourceSkipList $skipList -RetainPermissions
I tried to run it without removing the trusted identity token issuer but it kept erring out.