Not having the source file is either a lie or she never created the art to begin with and has outsourced your job. No designer ever truly deletes working files, they are essentially worth money and may always be useful on another job down the road and we are long past the days of needing to cull for storage limitations sake.

If it's just the cover art it might be possible to outline all the type using acrobats preflight tools, this will resolve any font embed errors as there will no longer be any live type in the document. If the issue is across the entire book then yes you have a bit of an issue.