I’ve never personally heard of issues like this arising from shipping a CompactFlash card, and I know many people use it as a way to quickly restore machines. Perhaps someone else has a different experience they can share.
However, it is good that the PLC is in Service mode. If the memory was corrupted, the target might end up in Diagnostic mode where Automation Runtime has failed to boot correctly. In Service mode, your program is fully installed but none of the cyclic tasks are running due to an application error (missing module with Module Supervision enabled, cycle time violation, etc.). You can see this post for more information. If you are able to diagnose remotely or get a log file from the customer, you should be able to figure out what’s going on and then you can compare to other machines that have the same problem.