Backup Restore w/ updated documents

If I do a backup restore on a collection and the backup has updated information on the existing documents, I get the duplicate _id error (E1000) and existing documents are not updated. However, I need to update the document with the latest data from the backup. Is there a way to do a restore on the existing collection that will see the duplicate _id but still insert the updated document from the backup without errors?

mongorestore performs only inserts.
mongoimport can do an insert, update or merge.

I had read that you should avoid using mongoimport and mongoexport for full instance production backups because they do not reliably preserve all rich BSON data types since JSON can only represent a subset of the types supported by BSON. Is mongoimport the only way to update all the documents w/o getting dup id errors? Thanks for the info btw

What I was highlighting is that a backup/restore process is not meant for updating or merging data. If you know that you’ll have collisions then you should drop and restore the collection. There’s a --drop option in mongorestore.

mongoimport and $merge are the only tools used for merging data.