This issue has been reported by quite a few others who have hit the same wall, some with files stuck for days and in a few cases up to three months.
The "In Progress" status means the platform is still processing your uploaded file before it becomes usable. For a single PDF this usually clears within a few minutes, so if it has been stuck for hours, something has likely gone wrong on the backend rather than it just being slow.
The quickest thing worth trying first is deleting the stuck entry, waiting about 10 minutes, then re-uploading. Sometimes the indexing job fails silently on the backend and a clean re-upload kicks it off properly. After re-uploading, make a small change to your agent like editing the description, save it, and republish. Community members have found that republishing can nudge a stalled job back into gear, as discussed here: https://community.powerplatform.com/forums/thread/details/?threadid=f4f3614a-1f21-f111-8341-7ced8dcf6124
Check your file as well. If the PDF is image-based with no text layer, the platform has to run OCR on it first which adds significant time and sometimes fails entirely. A PDF exported properly from Word or PowerPoint with a real text layer will index far more reliably than a scanned document. Also worth confirming that the file is not password-protected or encrypted, as those will block processing entirely regardless of file size.
One thing worth knowing about the SharePoint workaround: it is not fully immune to this issue either. Even via SharePoint, the status can flip from Ready back to In Progress before it finally settles. So it is a valid alternative path but not a guaranteed fix.
If the file stays stuck past 24 hours after a fresh re-upload, this needs a Microsoft support ticket. In confirmed cases, the resolution came from Microsoft reprovisioning the environment on the backend, which is not something you can trigger yourself: https://learn.microsoft.com/en-us/answers/questions/3863448/after-updating-the-solution-for-our-chatbot-in-pro
If you are on a Managed Environment, that has also been flagged by community members as a contributing factor worth mentioning to support when you raise the ticket.
Vishnu WR
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