Generally speaking, not every machine has the INI file in the same path, so Appeon deploys INI files to Appeon servers via the Appeon Developer. And please note that the INI files are saved and downloaded in XML to the client.
You can change the template file via AEM > Welcome > Application > PB Features > INI Files > [your_application] > INI File Content in the Appeon Server after they are deployed:
There are two modes to download and save the INI files to the client: Server-side (Web Only), and Client-side, and Appeon would recommend the Client side mode. You can set the mode in AEM > Welcome > Application > PB Features > INI Files > [your_application] > INI File Mode Settings. For details please read the local Appeon help in Appeon Help | Appeon Server Configuration Guide for .NET | AEM User Guide | Application | PB Features | INI Files | INI File Mode.
Please do not judge if the INI files exist in Appeon the way you judge them via FileExist in the PB C/S architecture as they are already deployed to the Appeon Server and saved and downloaded to the client in XML format.
And Appeon fully supports SetProfileString, ProfileString, and ProfileInt.