Backup error on database with unused or corrupt data

The backup process throws the following error, most likely due to corrupt or unused data. This problem was posted as an issue earlier and hasn't been resolved.

command failed: Backup failed: Error starting$GraphDatabaseFactoryWithPageCacheFactory$1, /disk2/neo4j-backup/default_backup/temp-copy

We did dump and load the database, and then cleaned up with store utils, however it resulted quite unexpectedly, destroyed all the relationships in the database and connected them to a single node with id 0. See the issue below:

So we are left helpless with a corrupt database, with no way to do proper backup (we have earlier backups that are ok but there are new data on production), no utils to clean. We use neo4j 3.5.5. We'd appretiate your suggestions on how to deal with these two issues? Thanks!