The backup tasks backs up everything, so my personal opinion is you’re overcomplicating the scenario by trying to split it.
My recommendation would be to split the servers instead if this works for your workflow, then you can just full back up one place without having to worry about hijinx and not backup the other at all.
As far as the reindexing, I’m not sure but I wonder if the backups (db & blobstore) are not taken at the same time. Reindexing (or repair) might be needed if there were discrepancies…it shouldn’t normally be needed as far as I know.
Ref https://help.sonatype.com/display/NXRM3/Prepare+a+Backup “The blob stores and metadata databases must be backed up together or the blob store metadata may be non-descript when attempting to restore the exported data.”
Some general thoughts,
-Joe Tom