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Not sure what you mean by "custom tags" and how you are trying to assign them on a Kobo ereader? Do you mean collections (aka shelves)? If so, you can use the Kobo Utilities Get Shelves From Device to read the collections on the Kobo into a custom column in calibre. Just remember that that data is read from the Kobo database so anything done in KOReader is a non-starter since that data is not stored in the Kobo database.
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