Right,
Inshort:
1. How do i get those independent disks backed up in VMware Data Recovery
Answer: You cant. Turn off Independent mode, after that you can em backup normally with VDR. Any particular reason you are using Independent Disks?
2. In case i have to restore the backed up VMs, am i going to get a VM minus those disks marked as independent?
Answer: Yes, only that what was backupped will be restored, the datadisks you made independent will have to be re-attached if the original OS-disk for example was corrupted and the datadisks were still fine.
In the large environment I work with we make backups of the contents of the VM from the VM itself (using EMC Networker & dedup with Avamar). A program like Veeam's Backup & Replication leverage the vStorage API's and a few other options, but effectively copy the vmdk-files and dedupelicate those.
So in your case you would either have to recreate the files like you suggested and restore from a filelevel backup system or restore vmdk-file from a backup system that backups those (like Veeam).
