WP html editor using page id for internal links

I’m doing some major work on a WordPress site I created a couple of years ago. I copied it to a development server using BackupBuddy. I’ve just noticed that the html editor is writing all the internal links with page IDs rather than page names. Everything works correctly and the IDs are transformed to page names in the source code, but I don’t remember ever seeing this before.

My big concern is that we’re going to turn this into multisite and clone the main site in order to create translated versions. If something is screwy now, I need to straighten it out.

Permalinks are using month and name. The pages' slugs are the right page name. I've reverted to the default permalinks and then back to the ones I'm using with no effect.

My deadline for getting the site back up is this Friday, so I'm in a big rush too, with a lot of last minute work.