WebAgent 6 version did not have Agentid.dat, but 12.5 version has this file.
What's Agentid.dat file for?
* AgentIdFile Specifies the path of the AgentId file which stores the unique ID string of the agent. The agent automatically generates the AgentId file, which must not be modified. Both on Windows and UNIX, the agent must have write permission to update the AgentId file.
On Windows, the Web Agent configuration wizard grants the write permission automatically.
The Agent ID was added to support the new feature added to R12.r Called Agent Discovery for more info on this feature please see documentation https://docops.ca.com/ca-single-sign-on/12-52-sp2/en/configuring/policy-server-configuration/agents-and-agent-groups/agent-discovery
The AgentID.dat file is created when completing the configuration process, but it is a process done by the Agent itself (and not the Wizard), so in case the file is missing, at the first Agent connection to Policy Server it should be recreated again.