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The metadata
is stored in the inode, you can request that data from windows (or the os), simply append the data to the beginning of the file (with magic numbers/markers at the beginning and end of the metadata) and encrypt as usual. After decryption extract the meta data that was appended and use it when creating the new decrypted file.
The metadata is just data, tack it on to the file and you'll have it available when your decrypting so it can be restored. It's no big deal.
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