** This issue is addressed in ArcGIS 9.0 Service Pack 3 (SP3) **
When using the Feature Project Tool in ArcToolbox, features at the edges of the data extent disappear and are not reprojected.
The reprojection includes a geographic (datum) transformation. A geographic transformation occurs when the input and output geographic coordinate systems differ. The input and output coordinate systems may be projected, as a geographic coordinate system is contained with a projected coordinate system.
When calculating the output xy domain, the geographic (datum) transformation was not used. This means that the output xy domain may not be large enough to contain all the features after the reprojection. Features that touch or cross outside the xy domain are not reprojected.