Correct, we want the "u" accounting record to represent incremental values.
An example: suppose job A runs 3 hours, initially starting on 4 nodes but releasing 1 node each hour. For this job I'd expect an S record, 2 u records, and an E record (I'll ignore other records like Q). The S record is fine as-is.
The first u record should contain resources_used.walltime=01:00:00, note the exec_host/vnode of the just-completed phase with 4 nodes, and provide exec_host/vnode of the new phase with 3 nodes. It should also include as many fields from the E/R record as are reasonable.
The second u record also contains resources_used.walltime=01:00:00, but has exec_host/vnode of the just-completed phase with 3 nodes, and provides exec_host/vnode of the new phase with 2 nodes. Again it should also include as many fields from the E/R record as are reasonable.
The pbs server will need to be smart and create the E record with resources_used.walltime=01:00:00 (rather than 03:00:00).