The possible reason can think of is e.g. lost connection with a network drive where the rtd file is saved or where cfg or cfgusr folder is located. It can also be caused by the rtd file being marked as read only.
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Robot was running on my notebook at home and I am sure with no network drive. At the moment the program works correctly so I cannot reproduce the error. If in the future the problem appears again I will check your suggestion.
The autoarch.err message appears quite consistently if I have two instances of RSA running and trying to save a project in the second instance. The save appears to be successfull though, so have not really worried about it.
You are competely right. I was working with two instances of Robot normally with the general model and a saved substrucure with additional constraint in order to analyze particular part of the model that is very big and my notebook is not so powerful.