It happened to me and a friend on Swiss Business Upgrades ticket. When claiming on line the missing miles, we got the Flug bereits erfasst mention. We therefore sent our BP to get the miles credited. I got them fairly quickly, while my friend got the flights credited more than 2 months later after e-mailing and calling them several time. I got it also on OS flights, but in this case it was because I claimed the missing miles 4 days after the flights and my claim may have crossed the credit as next day the credit came together with a second entry of the flight with the "Flug bereits erfasst" mention.
Would send my BP asap and if not credited within the next months then call.