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Please note the following from Martin Steigerwald of Haage & Partner:

Use a boot partition within the first 4GB of the hard drive as long as you are not absolutely sure that you really understand in which circumstances you can use a partition not within the first 4GB and are in absolute agreement to take the full responsibility on what you are doing and promise faithfully that you will not contact AmigaOS 3.9 support when something goes wrong.

Simply put, boot partitions beyond the first 4GB partitions are NOT officially supported, but can work under special circumstances at your own risk.