After installing Apple Photos as part of the 10.10.3 update and attempting to migrate my Aperture library I get an error message about "permissions" on my Aperture library:
What does this mean and why is it happening?
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.
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.