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In this section of the wiki, common errors will be layed out and will be walked through to fix them.
Check logs-errors section to learn more about a log error.
Please follow the following generic steps to troubleshoot your issue.
As of v.0.5.6 file structure changed due to the scanner update please do read how the new Scanner works
TLDR:
If you are sure your files are compliant, then something is going on. Put your logging level on Debug and redo process.
After that check the logs and take a look at logs-errors section.
Ensure you understand that pdfs, epubs and cb* do not stack in Kavita. Kavita separates by format -and series name due to different format having different readers
The root cause for this issue is that you probably have one series across multiple folders. Make sure your folder structure is compliant with scanning requirements