You can't use FFS2 on WinUAE. FFS2 is PPC only and can only be used with AmigaOS 4.0.
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Would it be possible to write the RDB and create several partitions
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It is not only possible, but necessary. If you don't create partitions, there is no sense in using it with WinUAE. AmigaDOS can only see partitions. If there are no partitions, the HDD remains invisible.
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and perhaps even install OS3.9 BB2 using WinUAE?
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If your A4000 has a 68060, a gfx card or a CD-ROM drive, you should rather install it on the real Amiga. Otherwise the OS might lock up or crash.