The current method of naming FileIDs (and interfile links) was introduced in Mif2Go Version 3.2. If you update a file created using an older version of Mif2Go, you might have to update all files that it references, and that reference the updated file. Otherwise you might encounter broken links, because the internal link identifiers might be using different FileIDs.
Note: Whenever FileIDs change, you must update settings in any configuration sections that reference the previous FileIDs, such as the [Graph*] sections.