You can do one of two things:
1) delete the converted file (or just move it to an archive folder as a backup), launch FileMaker Pro 11 and select ALL your 5 fields that make up your solution to be opened/converted at the same time. This should produce valid external file references in the new converted file copies.
2) Open your FMP 11 file and select manage | External data sources. From here you can find all external data source references for the customer database file and you can update them to refer to the new FMP 11 file.
I strongly recommend that you open and review Manage | external data sources regardless of which "fix" you choose to apply. FMP 5 was notorious for producing a real "rat's nest" of external data source references. FileMaker 11 will attempt to clean them, merging duplicate references, but you still may find quite a mess here. Your files should open correctly, but issues in these references may greatly slow how fast they open and they may be "cluttered" with out of date references to files and folders that no longer are part of your solution. FileMaker Advanced's database design report can be a big help in cleaning up and simplifying the external data source references left after the conversion is complete.
If you haven't already read it, this KB article on file conversion may be helpful: http://help.filemaker.com/app/answers/detail/a_id/750/kw/converting