Idk, I would think any formatting would be fine, and once booted into recovery, file operations should work, but it would be worth testing.
I'm not sure right now if the ps3 will boot into its own mode for a backup and hen will be disabled anyway. Then all files should be backed up on hdd. The hard disk is always formatted before a restore. With old backups you will loose hen >3.1.1 after a restore.
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On the other hand, it was of course an advantage that all files were stored on /dev_flash in Hen versions up to 3.1.1. This made HEN completely independent of backups. If new backups now contain files that will perhaps no longer fit in the future for new HEN Versions, problems are inevitable.
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Yes for new backups this is the best solution.