Check this link, all the restaurants mentioned there are supposed to open on Sunday.
It isn't a question of which restaurants are open for lunch on a Sunday in Auxerre but rather which ones are likely to be able to provide lunch within the time allotted for the coach stop. Sunday lunch in France is traditionally the time for a relaxed family lunch, and that is what many restaurants will still be geared to, rather than the more hectic pace of the working week lunch.
However, it has been my experience that most coach drivers have a very good idea where the restaurants are that will provide a quick lunch to a coach load of people, even on a Sunday, and I suspect that you will find the coach stops close by just such an establishment. It isn't impossible that you will find that it turns out to be the autoroute aire near, but not actually in, Auxerre.
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