Hi Paul,
It sounds like you have multiple issues going on. I highly suggest opening a support case to ensure that we get them all resolved.
1) About your configuration settings that does not allow a user to be logged into more than one client at a time. The Sametime 12 environment is designed to allow users to be logged into multiple clients at the same time. Now that we have persistent chat, it allows the users to receive the same chats in multiple clients. In old versions, such as v9 and earlier, which are before the persistent chat feature, only one client received the chat, hence the default in the older versions was to only allow the user to login to one client at a time.
A client login can be the rich client (Sametime Connect, embedded Notes client), web chat, mobile client or a meeting.
Do you want the new behavior (the default for Sametime 12)? There is a Sametime.ini parameter you can change to get it to use the new behavior (multiple client logins allowed). I believe if you simply remove it, that you will probably get the default.
This belongs in the Config section, VPS_BYPASS_SINGLE_MACHINE_LOGIN, setting it to 1 allows the user to login to multiple clients simultaneously, which is the default in Sametime 12. Setting it to zero will only allow the user to login to one client.
2) For the issue of not being able to login to the mobile client, you should first ensure that you can login to the webchat client. Use a browser such as Chrome, Edge or Firefox and enter the fully qualified domain name of the server followed by /chat (https://sametime.example.com/chat)
Additionally, on iOS devices Apple is very strict about the certificate used to secure the server. It needs to be trusted by the device. Are you using a certificate from a well known certificate authority?
3) Lastly, the warning message you are getting in the client regarding a change can be caused by multiple things. One of the more common reasons is incomplete or incorrect managed settings. It may have been you had an ST_COMMUNITY_ID set in the old environment and the setting was not carried over to the new environment. There could be other reasons also but I would need to see some logs. A case is best to work the issue.
Thank you,
Casey Toole
HCL