Finally coming back to this topic: First of all, thank you all again for the suggestions and proposed solutions.

I needed some days testing a few approaches and playing around with things. In the end I went with the solution holch suggested, uploading a participant table with an already defined token and including the relevant ID.

For anybody else stumbling over this topic with a similar problem: As stated above when running LimeSurvey in closed-access mode (that is you want to restrict access to participants with a token as an access key), you cannot pass id=%SURVEY_CODE% along as an URL parameter the way it is described in the manual.

The %SURVEY_CODE% that Sona Systems passes to LimeSurvey is contrary to what the name suggests not the ID of the survey, but rather an individual code for the participant (constant across studies). It is part of the participants list one can download from Sona Systems. When initialising a participants table, click on Manage attributes and add attribute_1 as the ID. Before uploading the participants list to LimeSurvey, simply change the name of survey_id in the file to attribute_1 (you also need to change first_name/last_name to firstname/lastname).

Then modify the End URL such that it ends with survey_code={TOKEN:ATTRIBUTE_1}. LimeSurvey will then simply import the participants's ID from the uploaded participants table and pass it back to Sona.