With FLAC files as with most audio file types, Yate does whatever it can to avoid rewriting an entire audio file. However, if the new metadata cannot be placed without rewriting the audio data, an entire write of the file will be necessary. Typically when adding artwork, especially if there was none before, there is insufficient free space to write the new metadata 'in place'. Depending on how large your files are and where they are stored, external drive, NAS drive, etc. this can take a long time.

You should be seeing the change indicators changing from Red to Green as the saving proceeds.

If you subsequently make minor changes to the metadata which does not drastically increase its size, the saving will be far, far faster.