When you update a version of FME, in most cases, this will not affect how you access custom formats. However, ArcGIS Data Interoperability users may need to perform an additional step.
When upgrading to a newer version of ArcGIS (for example, from 9.1 to 9.2), ArcGIS users must use a specific process in order to access custom formats:
Do not copy the format files (.fds) to the location: C:\<My Documents>\FME\Formats that ArcGIS 9.2 uses.
You must use the Import option in the Data Interoperability Formats Gallery and import your formats. Simply copying them over will not be effective since the formats will display in the Formats Gallery but the "Edit" button will be disabled.