One more reason for missing updates I can think of is that when the document is ingested into source index, its timestamp is "old", i.e.: older than 60s (the configured delay) than the actual server timestamp.
Usually the solution for that is to have an ingest pipeline on the source index that will populate event.ingested field for every source document and then to use event.ingested field in the sync.time section of the transform config.
You can find the pipeline code here: