Apple have an answer for you here: https://developer.apple.com/library/content/qa/qa1726/_index.html
Q: How do I resolve the Potential Loss of Keychain Access warning?
A:
Potential Loss of Keychain Access. The previous version of software has an application-identifier value of 'A1B2C3D4E5.com.company.app' and the new version of software being submitted has an application-identifier of '5E4D3C2B1A.com.company.app'. This will result in a loss of keychain access.
Note: This is a warning, not an error. You have the option of proceeding with the submission regardless of this warning, however this document should be used to determine whether you can safely ignore it.
This warning indicates that the App ID prefix of the pending submission differs from the App ID prefix of the live app in the app store.
Important: The only apps that can ignore this warning without consequences are those that do not use technologies that rely on the App ID prefix, like keychain access, Handoff, and UIPasteboard sharing.
Apps that should expect this warning and proceed with the submission regardless are:
Those that are migrating their App ID prefix from an arbitrary Bundle Seed ID to their more-modern Team ID as documented in Technical Note TN2311 - Managing Multiple App ID Prefixes.
Those that are submitting the first update for a recently acquired app via App Transfer.
Note: Apps receiving this warning due to App Transfer should read TN2311 > A one-time loss in keychain data will occur if you switch your App ID prefix and understand that it's not possible for a transferred app to maintain access to the prior keychain associated with the App ID prefix of the previous owner.
For apps that do utilize technologies that rely on the App ID prefix, this warning should not be ignored. The Potential Loss of Keychain Access warning is an indication that the app was code signed with the wrong provisioning profile.
To resolve the problem:
You must locate or re-create a provisioning profile that uses the correct App ID prefix on the Certs IDs & Profiles website.
Click Edit on the profile to be certain the prefix is correct.
Click Download and save the profile to disk.
Optionally double check the App ID Prefix on the downloaded profile using the Terminal command in: How do I check the entitlements associated with my Provisioning Profile?
Drag the profile onto the Xcode icon on your Dock to install it.
Re-submit the app and code sign it with the newly restored profile that is associated with the right prefix.
"Keychain access" refers to all the functions in the Keychain Services Reference.
