Your document (e.g., "filename.fadein") was created using an earlier version of Fade In. Versions of Fade In prior to v5.0.11 added "-updated" to an older-version file when opening it.
When a new major version of the software is released, the version of documents saved with it will match the new software version. Updating the document allows you to keep a backup of the copy in the previous version, if you so choose to.
Fade In is always able to open previous-version documents without issue.
You can always simply choose to re-save your document under the original name (i.e., saving "filename-updated.fadein" as the original name "filename.fadein").
Note: As of Fade In v5.0.11, the original older-version file will be optionally backed up on disk when opened, as "filename-backup-v#.#.fadein", instead of adding "-updated".