I've converted several extensive 5.5 database systems to version 10 and saw no such issues. The conversion to v11 should produce the same results.
How did you convert your files? Did you open and convert them as a group or one at a time? A set of related files should be opened and thus converted as a group to get the best possible external data source references.
Once conversion is complete, you can open Manage | External data sources in each converted file to inspect the references that exist to other files. You can then edit these references as needed to correct or improve how your files access other files.