Thanks for that Marcin.
I think the error is thrown after a user has been using Notes 8.5.3 via Citrix and then goes back to their Notes 9.0.1 client. They are seeing the error in the 9.0.1 client though. When they launch 8.5.3 it asks them for their ID file location.
After I re-run Notes setup on the 9.0.1 client the error goes.