Solutions
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OctoDev's post in Commerce; Updating groups does not work if many purchases was marked as the answerI ended up having to code a custom PHP Script that would access the database, it completed the task that took several hours to do 5 000 members - in 20 seconds of execution. Moved +100 000 members into correct groups...
Hope this feature can be improved so it can actually be used in the near future.
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OctoDev's post in Commerce "Purchase Benefits" not giving Secondary Group was marked as the answerFound the issue, it was a plugin.