Why do I need to "repair permissions" on my Aperture library in order to migrate to Photos?

Solution 1:

Apple often uses custom permissions to prevent users from going inside library files and deleting files that need to be in place since they are thumbnails and/or database files or referenced in database files.

Here's an official knowledge base article on the permissions required and steps to fix it.

• https://support.apple.com/en-us/HT204484

Reading your alert, the step is probably precautionary to ensure that all the files are readable and ready to transfer.

You can check the locking with Finder - select the Aperture Library and choose File -> Get Info. Observe the locked button and expand the Sharing & Permissions portion if needed. You probably need Read & Write permission on the folder and all it's contents. If you wanted to dive into terminal, I'd start at the bottom of the article and work upwards.

I would let the tool work and contact AppleCare if it reports another error or doesn't fix the permissions after one pass.