[Adoby]

Books are stored unchanged in calibre, if you update metadata and cover and so on. When you send to device or save to disk metadata and cover is updated in the new copy.

This ensures that you can keep your original ebooks unchanged and you can convert from the original to different formats and to different devices again and again with different settings without loss of data.

Calibre server serves the originals as they are stored, without updated metadata. This can, as you have discovered cause problems and surprises.

However, you CAN apply updated metadata and covers to the books as stored inside calibre. You use the function "Polish" to do so. You can add a "Polish" button bar to the main menu bar to make this easy to access.

Conversions also update metadata and cover, but only for the new format.

So this is not a bug. It is a feature... The original ebook is preserved by calibre until you decide it should be updated.