In the document Perform Maintenance on Replica Set Members, there is a step to start the secondary as a standalone on a different port.

It would be nice if we can add a note that we should use the same user (that we used to start this node as a member of the replica set) to start the secondary as a standalone instance. Otherwise, if the maintenance task creates new data files, the data files may be owned by a different user. When we start the mongod as a member of the replica set, it may have issue to open those data files. This could happen when we try to create a new index, or to change the size of system.profile collection, etc, during the maintenance.