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I asked because it maybe running into the "too many files in folder" problem that seems endemic to windows kernels/file systems. I suggest just using your workaround for the moment. calibre's conversion of html delibrately leaves the input file structure alone, to allow people that hand edit their files to preserve the structure.
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Notice to all: I can not provide assistance with DRM removal, for legal reasons, so please do not contact me about it.
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