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Assuming you kept the original unaltered image files you created before messing with copies of them in WinUAE, at least all your data will be safe. If you didn't... well, almost all your data is probably still recoverable at least. Just make sure to backup/archive the image files and only work with copies.
I guess it's possible that doing something in HDToolBox caused it to write to the disk/image, overwriting the A2090-type partition info. Could you attach the WinUAE config you're using?
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