There was a post about this issue on a Japanese forum. I tried again and confirmed that the problem could be reproduced.
Clicking on the 'Update page and section numbers' option does not solve the problem.

日本のフォーラムで、この件について投稿がありました。追試して、再現を確認しました。
click on the 'Update page and section numbers' option 　では解決しません。

https://community.adobe.com/%E8%B3%AA%E5%95%8F-243/%E3%83%96%E3%83%83%E3%82%AF%E3%83%91%E3%83%8D%E3%83%AB%E3%81%A8%E3%83%9A%E3%83%BC%E3%82%B8%E3%83%91%E3%83%8D%E3%83%AB%E3%81%AE%E8%A1%A8%E7%A4%BA%E3%81%A8-%E3%83%89%E3%82%AD%E3%83%A5%E3%83%A1%E3%83%B3%E3%83%88%E3%81%AE%E3%83%9A%E3%83%BC%E3%82%B8%E7%95%AA%E5%8F%B7%E3%81%AE%E9%A3%9F%E3%81%84%E9%81%95%E3%81%84%E3%81%AB%E3%81%A4%E3%81%84%E3%81%A6-388211

I also have 2024 files that I've opened in 2025 and saved them As to 2025. Then I create a new book and add those files to the new book. When opening the files that have page numbering set to auto from the book those files immediately become unsaved, although the page numbers are correct.

Using update page and section numbers on the book does NOT fix the problem.

If I then save the file it opens correctly from the book the next time.

***Is there anyway to tell what is changing when the file is opened from the book?

I found this problem also. It almost seems like it has something to do with the entry in the book. Simply updating the numbering doesn't seem to fix the problem, it still changes the number when it shouldn't. For instance if auto number is OFF in the book but is ON for the file. We do this so the number don't automatically update when we don't want them to, BUT we can still tell it to renumber.

If you remove the file from the book and add it back in again, or recreate the book entirely, the oddities seem to go away.

The weirdest thing when it's changing things to page 1 is that visually the numbers are wrong, but internally (like in the book pallet) they're correct. At least that's what I've found.

I have a book made in InDesign 2024 that I opened in ID2025. When I created the PDF of the entire book, every document started with page 1 even though the book palette showed the continued page numbering. I checked the documents and they said auto page numbering, but the numbers began at 1. I ended up converting the documents back to 2024 and creating a new book file in 2024. In 2024, the pdf exported with the proper page numbers. I use book files often. This will keep me away from 2025 until it is fixed. I have copies of the 2024 and 2025 files.

This is happening to me as well. Every book document, new and old, starts from page 1, even if it is removed and then readded to the book. I have reset my preferences, and this is happening even with fresh default settings. I have also tried editing the preference option that says "Use Absolute Numbering," but all this does is change the pages panel to also show pages starting from 1. I also have the books set to continue numbering from the previous document, but InDesign seems to be ignoring that.

The only solution I have found is to manually change the first page of each chapter to start numbering at the page I know it should be. This is obviously not ideal because if any preceding chapters change their page count, the chapter will still retain the old page number.

This is a bug, and it needs to be fixed immediately as this makes InDesign useless for anything other than single documents.

Indesign 20.0 book auto numbering broken. Drops pages in certain chapters so that page numbers do not conform to those shown in Book panel. Pages dropped may depend upon whether chapters end with an odd or even page. Had to set start number for chapters so that they would conform to page numbers shown in book panel.