Slightly unrelated question:
What happens when template includes a mapping for a variable to be cast as long, but variable comes in with quotes like "1024"? Does it get discarded? I noticed that the sum docs.count + docs.deleted are close to the total number of documents in the original index. So while there are still some documents completely missing from destination index this would at least explain part of it.
In my latest test out of 1151419 total documents, destination index contains docs.count = 684045 and docs.deleted = 196412. So while 270962 are still missing, at least 200k are simply deleted.
I also tried reindexing into a name that doesn't match any templates and all documents made it across. So while it might still be a bug worth reporting on GitHub I suspect I just don't have a full understanding of how mapping changes affect reindexing.