Sometimes LDS.org and MLS get out of sync. Does he always appear in, for example, Leader and Clerk Resources, or in the LDS Tools app, but doesn't show up in MLS? Or, are you looking at the same tool (for example, Leader and Clerk Resources) both times and sometimes see him but sometimes don't?
You can check if his records are moving in and out of the ward by going to Leader and Clerk Resources > Reports > Members Moved Out. If his records didn't move, most likely it's a problem with LDS.org and MLS getting out of sync.
Samuel Bradshaw • If you desire to serve God, you are called to the work.